T0448

protein Q88SR8 from Lactobacillus plantarum

Target sequence:

>T0448 Q88SR8, Lactobacillus plantarum, 232 residues
MIAMIVKGGLAMAISNGHVSFKRPAWLGDSITANNGLATVHYHDILAADWDVERSDNLGISGSTIGSRYDAMAVRYQAIPEDADFIAVFGGVNDYGRDQPLGQYGDCDMTTFYGALMMLLTGLQTNWPTVPKLFISAIHIGSDFGGSFSAVTNGLGYRQSDYEAAIAQMTADYGVPHLSLYRDAGMTFAIPAQAAIYSVDTLHPNNAGHRVIARKLQSFLDSHFLEHHHHHH

Structure:

Method: X-ray, res=2.12Å, R/Rfree=0.19/0.22

Determined by: NESG

PDB ID: 3dc7

3dc7_A cartoon
Cartoon diagram of 448: 3dc7 chain A residues

PyMOL of 3dc7

Domains: PyMOL of domains

Single domain protein.

Structure classification:

SGNH hydrolase from Flavodoxin-like fold.

CASP category:

Comparative modeling:medium.

Closest templates:

3bzw.

Target sequence - PDB file inconsistencies:

T0448 3dc7.pdb T0448.pdb PyMOL PyMOL of domains

T0448    1 MIAMIVKGGLAMAISNGHVSFKRPAWLGDSITANNGLATVHYHDILAADWDVERSDNLGISGSTIGSRYDAMAVRYQAIPEDADFIAVFGGVNDYGRDQPLGQYGDCDMTTFYGALMMLLTGLQTNWPTVPKLFISAIHIGSDFGGSFSAVTNGLGYRQSDYEAAIAQMTADYGVPHLSLYRDAGMTFAIPAQAAIYSVDTLHPNNAGHRVIARKLQSFLDSHFLEHHHHHH 232
           ~~~~~~~~~~~~~~~~~|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||~~
3dc7A   18 -----------------HVSFKRPAWLGDSITANNGLATVHYHDILAADWDVERSDNLGISGSTIGSRYDAMAVRYQAIPEDADFIAVFGGVNDYGRDQPLGQYGDCDMTTFYGALMMLLTGLQTNWPTVPKLFISAIHIGSDFGGSFSAVTNGLGYRQSDYEAAIAQMTADYGVPHLSLYRDAGMTFAIPAQAAIYSVDTLHPNNAGHRVIARKLQSFLDSHFLEHHHH-- 230

Residue change log: change 72, 109, 117, 118, 169, 186, MSE to MET;

Single domain protein: target 18-230 ; pdb 18-230

Sequence classification:

SGNH_hydrolase in CDD.

Server predictions:

T0448:pdb 18-230:seq 18-230:CM_medium; alignment

distribution of
first scores
First models for T0448: Gaussian kernel density estimation for GDT-TS scores of the first server models, plotted at various bandwidths (=standard deviations). The GDT-TS scores are shown as a spectrum along the horizontal axis: each bar represents first server model. The bars are colored green, gray and black for top 10, bottom 25% and the rest of servers. The family of curves with varying bandwidth is shown. Bandwidth varies from 0.3 to 8.2 GDT-TS % units with a step of 0.1, which corresponds to the color ramp from magenta through blue to cyan. Thicker curves: red, yellow-framed brown and black, correspond to bandwidths 1, 2 and 4 respectively.

click on a score in the table below to display the model in PyMOL

#	GROUP ↓	TS ↓	TR ↓	CS ↓	TS ↓	TR ↓	CS ↓	TS ↓	TR ↓	CS ↓	TS ↓	TR ↓	CS ↓	↓ GROUP	#
		T0448			T0448			T0448			T0448
		First score			First Z-score			Best score			Best Z-score
1	BAKER−ROBETTA	76.29	71.36	67.18	1.55	1.66	1.49	76.29	71.36	67.18	1.28	1.30	1.21	BAKER−ROBETTA	1
2	HHpred4	76.06	70.34	68.14	1.52	1.55	1.60	76.06	70.34	68.14	1.25	1.17	1.34	HHpred4	2
3	HHpred5	75.94	71.56	69.44	1.51	1.68	1.75	75.94	71.56	69.44	1.23	1.32	1.52	HHpred5	3
4	HHpred2	75.70	69.21	67.89	1.48	1.44	1.57	75.70	69.21	67.89	1.20	1.04	1.31	HHpred2	4
5	FFASsuboptimal	75.47	70.15	66.61	1.45	1.53	1.42	75.82	71.52	67.44	1.22	1.32	1.25	FFASsuboptimal	5
6	PS2−server	74.41	68.70	62.54	1.33	1.38	0.95	74.41	68.70	62.54	1.02	0.97	0.56	PS2−server	6
7	GS−KudlatyPred	73.94	69.17	66.10	1.28	1.43	1.36	73.94	69.17	66.10	0.95	1.03	1.06	GS−KudlatyPred	7
8	FFASstandard	73.94	68.31	65.50	1.28	1.34	1.29	73.94	68.94	65.55	0.95	1.00	0.98	FFASstandard	8
9	LEE−SERVER	73.94	64.94	67.98	1.28	0.98	1.58	75.35	68.70	68.16	1.15	0.97	1.35	LEE−SERVER	9
10	FAMSD	73.83	69.21	63.09	1.26	1.44	1.02	73.83	69.21	64.59	0.94	1.04	0.85	FAMSD	10
11	RAPTOR	73.83	63.89	66.03	1.26	0.87	1.35	74.18	69.01	66.76	0.99	1.01	1.15	RAPTOR	11
12	FFASflextemplate	73.47	68.94	65.55	1.22	1.41	1.30	73.94	68.94	65.55	0.95	1.00	0.98	FFASflextemplate	12
13	Fiser−M4T	73.24	64.32	61.65	1.19	0.92	0.85	73.24	64.32	61.65	0.85	0.44	0.44	Fiser−M4T	13
14	keasar−server	73.00	68.08	65.38	1.17	1.32	1.28	73.94	68.86	65.56	0.95	0.99	0.98	keasar−server	14
15	pipe_int	73.00	68.08	63.72	1.17	1.32	1.09	73.00	68.08	63.72	0.82	0.90	0.73	pipe_int	15
16	GS−MetaServer2	73.00	67.61	65.51	1.17	1.27	1.29	73.00	67.61	65.51	0.82	0.84	0.98	GS−MetaServer2	16
17	3D−JIGSAW_AEP	72.89	67.80	64.06	1.15	1.29	1.13	72.89	67.80	64.06	0.80	0.86	0.77	3D−JIGSAW_AEP	17
18	fais−server	72.89	66.39	65.57	1.15	1.14	1.30	72.89	66.39	65.57	0.80	0.69	0.98	fais−server	18
19	SAM−T02−server	72.77	66.59	63.52	1.14	1.16	1.07	72.77	66.59	63.52	0.79	0.72	0.70	SAM−T02−server	19
20	SAM−T06−server	69.60	58.88	63.02	0.77	0.34	1.01	72.77	66.75	63.34	0.79	0.74	0.67	SAM−T06−server	20
21	CpHModels	69.48	64.63	57.82	0.76	0.95	0.41	69.48	64.63	57.82	0.32	0.48	-0.10	CpHModels	21
22	MULTICOM−CMFR	68.19	56.14	61.18	0.61	0.05	0.80	70.19	63.54	61.35	0.42	0.34	0.40	MULTICOM−CMFR	22
23	Pushchino	67.37	62.44	48.61	0.52	0.72	-0.65	67.37	62.44	48.61	0.02	0.21	-1.38	Pushchino	23
24	YASARA	66.90	60.17	56.50	0.46	0.48	0.26	69.72	63.54	59.72	0.36	0.34	0.17	YASARA	24
25	MULTICOM−REFINE	66.43	59.47	58.31	0.41	0.41	0.47	66.43	59.47	58.31	-0.11	-0.15	-0.03	MULTICOM−REFINE	25
26	3DShot2	64.79	55.09	52.02	0.22	-0.06	-0.25	64.79	55.09	52.02	-0.34	-0.69	-0.90	3DShot2	26
27	Phyre_de_novo	62.68	57.67	53.60	-0.03	0.22	-0.07	66.43	59.16	54.68	-0.11	-0.19	-0.53	Phyre_de_novo	27
28	Zhang−Server	62.32	53.09	56.49	-0.07	-0.27	0.26	72.53	65.02	65.00	0.75	0.52	0.91	Zhang−Server	28
29	pro−sp3−TASSER	60.91	50.31	51.64	-0.23	-0.56	-0.30	60.91	50.31	56.25	-0.89	-1.27	-0.31	pro−sp3−TASSER	29
30	METATASSER	60.09	43.66	52.68	-0.33	-1.26	-0.18	63.97	55.05	56.38	-0.46	-0.69	-0.30	METATASSER	30
31	FEIG	59.62	48.20	53.21	-0.38	-0.78	-0.12	60.33	53.99	53.21	-0.97	-0.82	-0.74	FEIG	31
32	MULTICOM−RANK	59.51	51.84	50.97	-0.39	-0.40	-0.37	66.90	58.73	58.91	-0.04	-0.24	0.06	MULTICOM−RANK	32
33	MULTICOM−CLUSTER	59.51	51.84	50.97	-0.39	-0.40	-0.37	70.19	65.96	60.56	0.42	0.64	0.29	MULTICOM−CLUSTER	33
34	COMA−M	59.27	50.59	51.86	-0.42	-0.53	-0.27	59.62	53.91	51.86	-1.07	-0.83	-0.93	COMA−M	34
35	Pcons_multi	59.16	50.94	51.96	-0.43	-0.50	-0.26	59.16	51.56	51.96	-1.14	-1.12	-0.91	Pcons_multi	35
36	MUProt	58.57	53.09	50.50	-0.50	-0.27	-0.43	66.90	60.56	59.31	-0.04	-0.02	0.11	MUProt	36
37	BioSerf	58.33	49.34	51.88	-0.53	-0.66	-0.27	58.33	49.34	51.88	-1.25	-1.39	-0.92	BioSerf	37
38	Distill	58.10	51.29	49.46	-0.56	-0.46	-0.55	59.04	51.29	49.46	-1.15	-1.15	-1.26	Distill	38
39	Pcons_local	57.86	47.85	45.80	-0.58	-0.82	-0.97	57.86	47.85	46.46	-1.32	-1.57	-1.68	Pcons_local	39
40	SAM−T08−server	57.28	49.22	50.57	-0.65	-0.68	-0.42	75.23	71.01	66.78	1.13	1.25	1.15	SAM−T08−server	40
41	Pcons_dot_net	57.16	50.98	46.80	-0.66	-0.49	-0.85	58.33	53.17	48.90	-1.25	-0.92	-1.34	Pcons_dot_net	41
42	Phyre2	57.04	51.41	49.43	-0.68	-0.45	-0.55	66.31	60.05	53.76	-0.13	-0.08	-0.66	Phyre2	42
43	PSI	56.69	51.29	46.73	-0.72	-0.46	-0.86	56.69	51.29	49.50	-1.48	-1.15	-1.26	PSI	43
44	MUSTER	56.57	49.69	50.50	-0.73	-0.63	-0.43	56.57	49.69	50.50	-1.50	-1.34	-1.12	MUSTER	44
45	Poing	56.45	48.71	49.33	-0.75	-0.73	-0.56	66.78	58.18	54.15	-0.06	-0.31	-0.61	Poing	45
46	3D−JIGSAW_V3	56.22	50.74	45.82	-0.77	-0.52	-0.97	72.42	67.88	63.37	0.74	0.87	0.68	3D−JIGSAW_V3	46
47	Phragment	56.22	50.51	49.25	-0.77	-0.54	-0.57	66.43	59.39	53.74	-0.11	-0.16	-0.66	Phragment	47
48	ACOMPMOD	55.40	44.52	45.85	-0.87	-1.17	-0.96	55.40	46.63	45.85	-1.67	-1.72	-1.76	ACOMPMOD	48
49	GeneSilicoMetaServer	54.81	48.40	46.75	-0.94	-0.76	-0.86	56.92	48.40	46.75	-1.45	-1.50	-1.64	GeneSilicoMetaServer	49
50	circle	54.70	43.90	44.38	-0.95	-1.24	-1.13	73.94	69.17	64.44	0.95	1.03	0.83	circle	50
51	mGenTHREADER	53.17	47.53	43.96	-1.13	-0.86	-1.18	53.17	47.53	43.96	-1.98	-1.61	-2.03	mGenTHREADER	51
52	LOOPP_Server	52.11	45.77	43.54	-1.25	-1.04	-1.23	67.02	62.79	58.17	-0.03	0.25	-0.05	LOOPP_Server	52
53	3Dpro	52.11	41.59	48.69	-1.25	-1.48	-0.64	70.42	65.73	61.99	0.45	0.61	0.49	3Dpro	53
54	forecast	51.99	44.01	42.85	-1.26	-1.23	-1.31	52.11	45.54	49.24	-2.13	-1.85	-1.29	forecast	54
55	nFOLD3	51.99	42.84	43.96	-1.26	-1.35	-1.18	72.42	67.80	63.78	0.74	0.86	0.74	nFOLD3	55
56	COMA	51.76	44.95	45.14	-1.29	-1.13	-1.04	60.33	52.66	51.86	-0.97	-0.98	-0.93	COMA	56
57	FUGUE_KM	50.70	46.71	35.26	-1.41	-0.94	-2.18	56.34	48.20	42.21	-1.53	-1.52	-2.27	FUGUE_KM	57
58	FOLDpro	50.59	37.68	39.50	-1.42	-1.90	-1.69	52.70	45.34	45.79	-2.05	-1.87	-1.77	FOLDpro	58
59	panther_server	49.65	43.70	38.40	-1.53	-1.26	-1.82	54.46	46.48	44.20	-1.80	-1.73	-1.99	panther_server	59
60	rehtnap	48.83	44.29	30.44	-1.63	-1.20	-2.73	51.06	45.15	33.45	-2.28	-1.90	-3.49	rehtnap	60
61	FALCON_CONSENSUS	48.59	41.55	42.01	-1.66	-1.49	-1.40	74.30	68.35	66.27	1.00	0.93	1.08	FALCON_CONSENSUS	61
62	FALCON	48.59	41.55	42.01	-1.66	-1.49	-1.40	58.69	48.44	66.27	-1.20	-1.50	1.08	FALCON	62
63	MUFOLD−Server	38.97	32.63	27.76	-2.77	-2.43	-3.04	38.97	32.63	27.76	-3.99	-3.42	-4.29	MUFOLD−Server	63
64	mariner1	23.83	19.52	19.32	-4.52	-3.82	-4.01	55.05	46.28	50.00	-1.72	-1.76	-1.19	mariner1	64
65	MUFOLD−MD	17.61	15.65	22.19	-5.24	-4.22	-3.68	19.13	16.12	25.72	-6.79	-5.43	-4.57	MUFOLD−MD	65
66	RBO−Proteus	15.26	13.81	21.30	-5.51	-4.42	-3.78	15.26	13.81	22.20	-7.33	-5.72	-5.06	RBO−Proteus	66
67	RANDOM	12.48	10.50	12.48	-5.83	-4.77	-4.79	12.48	10.50	12.48	-7.73	-6.12	-6.42	RANDOM	67
68	OLGAFS	9.27	7.86	-5.34	-6.20	-5.05	-6.84	9.27	7.86	-5.34	-8.18	-6.44	-8.90	OLGAFS	68
69	BHAGEERATH				-5.83	-4.77	-4.79				-7.73	-6.12	-6.42	BHAGEERATH	69
70	Frankenstein				-5.83	-4.77	-4.79				-7.73	-6.12	-6.42	Frankenstein	70
71	huber−torda−server				-5.83	-4.77	-4.79				-7.73	-6.12	-6.42	huber−torda−server	71
72	mahmood−torda−server				-5.83	-4.77	-4.79				-7.73	-6.12	-6.42	mahmood−torda−server	72
73	schenk−torda−server				-5.83	-4.77	-4.79				-7.73	-6.12	-6.42	schenk−torda−server	73
74	test_http_server_01				-5.83	-4.77	-4.79				-7.73	-6.12	-6.42	test_http_server_01	74

X-ray Targets
387	388	389	390
391	392	393	394
395	396	397	398
399	400	401	402
403	404	405	406
407	408	409	410
411	412	413	414
415	416	417	418
419	420	421	422
423	424	425	426
427	428	429	430
431	432	433	434
435	436	438	439
440	441	442	443
444	445	446	447
448	449	450	451
452	453	454	455
456	457	458	459
461	463	465	470
477	478	479	481
483	485	486	487
488	489	490	491
493	494	495	496
497	501	502	503
504	505	506	507
508	509	510	511
512	513	514