Evolutionary classification of protein domain structures

alpha arraysalpha-helix arrays with mainly perpendicular helices

alpha bundlesalpha-helix bundles with mainly parallel helices

alpha superhelicesrepeating alpha-helix hairpins form a superhelix

alpha duplicates or obligate multimersalpha duplicates or monomers associate together to form a compact domain

alpha complex topologyalpha domain with complex and unique topology that cannot be described as array or bundle or superhelix

beta barrelssingle beta-sheet folded upon itself to form a barrel

beta meanderssingle beta-sheet with mainly meander topology

beta sandwichestwo beta-sheets stacked together to form a sandwich

beta duplicates or obligate multimersbeta duplicates or monomers associate together to form a compact domain

beta complex topologybeta domains with complex and unique topology that cannot be described as barrel or sandwich or meander

a+b two layersone alpha-helix layer and one beta-sheet layer

a+b three layersone mainly antiparallel beta-sheet layer sandwiched between two alpha-helix layers

a+b four layerstwo beta-sheet layers sandwiched between two alpha-helix layers

a+b complex topologyalpha and beta domain with complex and unique topology that cannot be described in layers

a+b duplicates or obligate multimersalpha and beta duplicates or monomers associated together to form a compact domain

a/b barrelsrepeating beta-alpha units form a barrel

a/b three-layered sandwichesrepeating beta-alpha units form a sandwich with a mainly parallel beta-sheet layer stacked between two alpha-helix layers

X: Rossmann-like

X: C-terminal domain in CAC2185-like proteins

X: P-loop domains-like

X: EreA/ChaN-like

X: HUP domain-like

X: HAD domain-like

X: Flavodoxin-like

X: Nucleic acid-binding domain of nonstructural protein 3

X: EDD domain

X: Phosphorylase/hydrolase-like

X: LigB-like

X: Other Rossmann-like structures with the crossover

X: N-terminal domain in NTD biosynthesis operon protein NtdA

X: Flavivirus non-structural protein 1 (NS1) a/b domain

X: STT3/PglB/AglB core domain

X: C-terminal domain in arabinosyltransferase C

X: Nqo1 FMN-binding domain-like

X: beta-carbonic anhydrase-like

X: a/b domain in QueA-like proteins (Pfam 02547)

X: a/b domain in AF0625-like proteins

X: CbiG linker domain

X: CobE/CbiG C-terminal domain-like

X: a/b domain in CV3147-like proteins

X: alpha/beta knot

X: Peptidyl-tRNA hydrolase II

X: Subtilisin-like

X: Insert domain in hypothetical protein PF0380

X: a/b domain in flagellar biosynthesis protein flhA

X: a/b domain in family 98 glycoside hydrolases

X: UPF0302 protein BA_1542/GBAA1542/BAS1430

X: Cellulose Synthase Subunit B a/b domain

X: Core protein P7

X: Type III R-M system modification subunit C-terminal domain

X: Restriction endonuclease-like

X: ClpP/crotonase

X: The "swivelling" beta/beta/alpha domains

X: Barstar (barnase inhibitor)

X: Ribosomal protein L13/L15p/L18e/L32e

X: C-terminal subdomain in Lon-related proteases catalytic domains

X: Atg7 N-terminal domain-like

X: MurF and HprK N-domain-like

X: DTD-like

X: Cell-division inhibitor MinC, N-terminal domain

X: CRISPR-associated Csx3

X: SpoIIaa-like

X: Small protrusion domain in cytoplasmic polyhedrosis virus capsid shell protein

X: Polycomb protein Eed insertion domain

X: HSP90 C-terminal a/b domain

X: STING C-terminal domain

X: C-terminal domain of poxin

X: Glycerate kinase I (Pfam 02595) domain II

X: Dihydrofolate reductases

X: Anticodon-binding domain of Class II aaRS

X: TolB, N-terminal domain

X: ITPase-like

X: Kinesin-like protein KIF23 C-terminal domain

X: N-terminal domain of GerK3 germinant receptor

X: Glutaminase/Asparaginase C-terminal domain

X: O-glucosyltransferase rumi N-terminal domain

X: NIF3 (NGG1p interacting factor 3)-like

X: Isocitrate/Isopropylmalate dehydrogenase-like

X: Single-stranded-DNA-specific exonuclease RecJ C-terminal domain

X: UDP-Glycosyltransferase/glycogen phosphorylase

X: CofD-like

X: Ferredoxin reductase-like, C-terminal NADP-linked domain

X: Alkaline phosphatase-like

X: Nucleotide-diphospho-sugar transferases

X: Nucleoside hydrolase

X: PK C-terminal domain-like

X: ATP synthase (F1-ATPase), gamma subunit

X: CinA-like

X: B12-dependent dehydratase associated subunit

X: TK C-terminal domain-like

X: Periplasmic binding protein-like II

X: ALDH-like

X: Phosphoglycerate mutase-like

X: Initiation factor IF2/eIF5b, domain 3

X: SurE-like/CoA-transferase family III (CaiB/BaiF)

X: Phosphoglucomutase, first 3 domains

X: Macro domain-like

X: Replicase polyprotein 1a N-terminal macro-like domain

X: Carbamate kinase-like

X: Phosphoglycerate kinase domain 1

X: Phosphoglycerate kinase domain 2

X: Undecaprenyl diphosphate synthase

X: Dipeptide transport protein

X: GckA/TtuD-like domain 1

X: PTS IIb component

X: Hypothetical protein MT938 (MTH938)

X: Creatininase

X: Bacterial fluorinating enzyme, N-terminal domain

X: Molybdenum cofactor biosynthesis proteins

X: Aconitase iron-sulfur domain

X: Methylglyoxal synthase-like

X: Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain

X: YchN-like

X: Glutaminase/Asparaginase N-terminal domain

X: Hypothetical protein TT1679

X: Methylesterase CheB, C-terminal domain

X: Indigoidine synthase A-like (Pfam 04227)

X: Tetrapyrrole methylase N-terminal domain

X: ComB-like

X: Amidase signature (AS) enzymes

X: Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT)

X: 2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, substrate-binding domain

X: Alpha-2,3/8-sialyltransferase CstII-related

X: Fe-only hydrogenase

X: DNA polymerase III psi subunit

X: Glycerol-3-phosphate (1)-acyltransferase

X: Ribosomal protein L4

H: Ribosomal protein L4

T: Ribosomal protein L4

F: Ribosomal_L4,Ribos_L4_asso_C

PF00573 PF14374

F: Ribosomal_L4

PF00573

Representatives:

e1dmgA1[A:2-42,A:96-226] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RIBOSOMAL PROTEIN L4 ; ligands: CIT ; X-RAY DIFFRACTION 1.7Å

e1vqoC1[C:1-246] nonrep Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

50S RIBOSOMAL PROTEIN L4E ; ligands: MG,NA ; X-RAY DIFFRACTION 2.2Å

e1qvgC1[C:1-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

50S ribosomal protein L4E ; ligands: MG,NA ; X-RAY DIFFRACTION 2.8Å

e1n8rE1[E:1-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

50S ribosomal protein L4E ; ligands: MG,NA ; X-RAY DIFFRACTION 3.00Å

e1vq4C1[C:1-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

50S RIBOSOMAL PROTEIN L4E ; ligands: MG,NA ; X-RAY DIFFRACTION 2.7Å

e1kc8E1[E:1-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RIBOSOMAL PROTEIN L4 ; ligands: MG,NA ; X-RAY DIFFRACTION 3.01Å

e1s72C1[C:1-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

50S ribosomal protein L4E ; ligands: MG,NA ; X-RAY DIFFRACTION 2.400Å

e1q86E1[E:1-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

50S ribosomal protein L4E ; ligands: MG,NA ; X-RAY DIFFRACTION

e1kqsC1[C:1-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed,

RIBOSOMAL PROTEIN L4 ; ligands: MG,NA ; X-RAY DIFFRACTION 3.1Å

e1q81E1[E:1-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

50S ribosomal protein L4E ; ligands: MG,NA ; X-RAY DIFFRACTION

e1yi2C1[C:1-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

50S ribosomal protein L4E ; ligands: MG,NA ; X-RAY DIFFRACTION 2.65Å

e1vq9C1[C:1-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

50S RIBOSOMAL PROTEIN L4E ; ligands: MG,NA ; X-RAY DIFFRACTION 2.4Å

e1yitC1[C:1-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

50S RIBOSOMAL PROTEIN L4E ; ligands: MG,NA ; X-RAY DIFFRACTION 2.8Å

e1vq7C1[C:1-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

50S ribosomal protein L4E ; ligands: MG,NA ; X-RAY DIFFRACTION 2.500Å

e1vq8C1[C:1-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

50S RIBOSOMAL PROTEIN L4E ; ligands: MG,NA ; X-RAY DIFFRACTION 2.2Å

e1yhqC1[C:1-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

50S ribosomal protein L4E ; ligands: MG,NA ; X-RAY DIFFRACTION 2.40Å

e2b66F1[F:1-168,F:193-246] Image Pymol Jmol Links: PDB, SCOP, CATH Obsolete PDB

e1yjnC1[C:1-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

50S ribosomal protein L4E ; ligands: MG,NA ; X-RAY DIFFRACTION 3.00Å

e1ffkC1[C:1-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RIBOSOMAL PROTEIN L4 ; X-RAY DIFFRACTION 2.4Å

e1vqmC1[C:1-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

50S ribosomal protein L4E ; ligands: MG,NA ; X-RAY DIFFRACTION 2.3Å

e1jj2C1[C:1-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RIBOSOMAL PROTEIN L4 ; ligands: MG,NA ; X-RAY DIFFRACTION 2.4Å

e1vq5C1[C:1-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

50S RIBOSOMAL PROTEIN L4E ; ligands: MG,NA ; X-RAY DIFFRACTION 2.6Å

e2b9nF1[F:1-168,F:193-246] Image Pymol Jmol Links: PDB, SCOP, CATH Obsolete PDB

e1yijC1[C:1-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

50S ribosomal protein L4E ; ligands: MG,NA ; X-RAY DIFFRACTION 2.60Å

e2otlC1[C:1-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

50S ribosomal protein L4P ; ligands: MG,NA ; X-RAY DIFFRACTION 2.70Å

e1vqpC1[C:1-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

50S RIBOSOMAL PROTEIN L4E ; ligands: MG,NA,SR ; X-RAY DIFFRACTION 2.25Å

e1yj9C1[C:1-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

50S ribosomal protein L4E ; ligands: MG,NA ; X-RAY DIFFRACTION 2.90Å

e1q82E1[E:1-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

50S ribosomal protein L4E ; ligands: MG,NA ; X-RAY DIFFRACTION

e1vqkC1[C:1-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

50S RIBOSOMAL PROTEIN L4E ; ligands: MG,NA,SR ; X-RAY DIFFRACTION 2.3Å

e1vq6C1[C:1-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

50S RIBOSOMAL PROTEIN L4E ; ligands: MG,NA ; X-RAY DIFFRACTION 2.7Å

e1qvfC1[C:1-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

50S ribosomal protein L4E ; ligands: MG,NA ; X-RAY DIFFRACTION 3.1Å

e2qa4C1[C:1-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

50S RIBOSOMAL PROTEIN L4P ; ligands: MG,NA ; X-RAY DIFFRACTION 3.0Å

e1vqnC1[C:1-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

50S RIBOSOMAL PROTEIN L4E ; ligands: MG,NA ; X-RAY DIFFRACTION 2.4Å

e1vqlC1[C:1-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

50S ribosomal protein L4E ; ligands: MG,NA,SR ; X-RAY DIFFRACTION 2.3Å

e1q7yE1[E:1-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

50S ribosomal protein L4E ; ligands: MG,NA ; X-RAY DIFFRACTION

e1k73E1[E:1-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RIBOSOMAL PROTEIN L4 ; ligands: MG,NA ; X-RAY DIFFRACTION 3.01Å

e1njiE1[E:1-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

50S RIBOSOMAL PROTEIN L4E ; ligands: MG,NA ; X-RAY DIFFRACTION 3.0Å

e2qexC1[C:1-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

50S ribosomal protein L4P ; ligands: MG,NA ; X-RAY DIFFRACTION 2.800Å

e1kd1E1[E:1-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RIBOSOMAL PROTEIN L4 ; ligands: MG,NA,SPR ; X-RAY DIFFRACTION 3.0Å

e2b9pF1[F:1-168,F:193-246] Image Pymol Jmol Links: PDB, SCOP, CATH Obsolete PDB

e1yjwC1[C:1-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

50S RIBOSOMAL PROTEIN L4E ; ligands: MG,NA ; X-RAY DIFFRACTION 3.000Å

e1yl3F1[F:1-168,F:193-246] Image Pymol Jmol Links: PDB, SCOP, CATH Obsolete PDB

e1m1kE1[E:1-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RIBOSOMAL PROTEIN L4 ; ligands: MG,NA ; X-RAY DIFFRACTION 3.2Å

e1k8aE1[E:1-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RIBOSOMAL PROTEIN L4 ; ligands: MG,NA ; X-RAY DIFFRACTION 3.0Å

e1m90E1[E:1-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RIBOSOMAL PROTEIN L4 ; ligands: MG,NA ; X-RAY DIFFRACTION 2.8Å

e2otjC1[C:1-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

50S ribosomal protein L4P ; ligands: MG,NA ; X-RAY DIFFRACTION 2.850Å

e1k9mE1[E:1-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RIBOSOMAL PROTEIN L4 ; ligands: MG,NA ; X-RAY DIFFRACTION 3.0Å

e3cxcC1[C:1-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

RIBOSOMAL PROTEIN L4 ; ligands: MG,NA ; X-RAY DIFFRACTION 3.0Å

e3ow2C1[C:1-246] Image Pymol Jmol Links: PDB, SCOP, CATH

50S RIBOSOMAL PROTEIN L4P ; ligands: MG,NA ; X-RAY DIFFRACTION 2.7Å

e3j21D1[D:1-255] Image Pymol Jmol Links: PDB, SCOP, CATH Obsolete PDB

e1w2bC1[C:1-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

50S RIBOSOMAL PROTEIN L4P ; ligands: MG,NA ; X-RAY DIFFRACTION 3.500Å

e1giyF1[F:1-168,F:193-246] Image Pymol Jmol Links: PDB, SCOP, CATH Obsolete PDB

e1ml5f1[f:1-168,f:193-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

50S RIBOSOMAL PROTEIN L4 ; ELECTRON MICROSCOPY

e3j44D1[D:1-255] Image Pymol Jmol Links: PDB, SCOP, CATH Obsolete PDB

e4v42BF1[BF:1-168,BF:193-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

50S RIBOSOMAL PROTEIN L4 ; X-RAY DIFFRACTION 5.0Å

e4v4nAD1[AD:1-255] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

50S ribosomal protein L4P ; ELECTRON MICROSCOPY

e4v4pAF1[AF:1-168,AF:193-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

50S ribosomal protein L4 ; X-RAY DIFFRACTION 5.50Å

e4v4rBF1[BF:1-168,BF:193-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

50S ribosomal protein L4 ; X-RAY DIFFRACTION 5.9Å

e4v4sBF1[BF:1-168,BF:193-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

50S ribosomal protein L4 ; X-RAY DIFFRACTION 6.76Å

e4v4tBF1[BF:1-168,BF:193-246] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

50S ribosomal protein L4 ; X-RAY DIFFRACTION 6.46Å

e4v6uBD1[BD:1-255] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI

50S ribosomal protein L4P ; ELECTRON MICROSCOPY

e4wweD1[D:1-207] Image Pymol Jmol Links: PDB, SCOP, CATH Obsolete PDB

e4wwtD1[D:1-207] Image Pymol Jmol Links: PDB, SCOP, CATH Obsolete PDB

e4wpoAF1[AF:6-208] Image Pymol Jmol Links: PDB, SCOP, CATH, PubMed, DOI