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3SQG
Biol. Unit 1
Info
Asym.Unit (1.2 MB)
Biol.Unit 1 (844 KB)
Biol.Unit 2 (844 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF A METHYL-COENZYME M REDUCTASE PURIFIED FROM BLACK SEA MATS
Authors
:
S. Shima, M. Krueger, T. Weinert, U. Demmer, R. K. Thauer, U. Ermler
Date
:
05 Jul 11 (Deposition) - 30 Nov 11 (Release) - 27 May 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I
Biol. Unit 1: A,B,C,D,E,F (1x)
Biol. Unit 2: G,H,I (2x)
Keywords
:
Anaerobic Methane Oxidation, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Shima, M. Krueger, T. Weinert, U. Demmer, J. Kahnt, R. K. Thauer, U. Ermler
Structure Of A Methyl-Coenzyme M Reductase From Black Sea Mats That Oxidize Methane Anaerobically.
Nature V. 481 98 2011
[
close entry info
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Hetero Components
(12, 32)
Info
All Hetero Components
01a: 7-HYDROXY-L-TRYPTOPHAN (0AFa)
01b: 7-HYDROXY-L-TRYPTOPHAN (0AFb)
01c: 7-HYDROXY-L-TRYPTOPHAN (0AFc)
02a: PENTAETHYLENE GLYCOL (1PEa)
02b: PENTAETHYLENE GLYCOL (1PEb)
02c: PENTAETHYLENE GLYCOL (1PEc)
02d: PENTAETHYLENE GLYCOL (1PEd)
02e: PENTAETHYLENE GLYCOL (1PEe)
02f: PENTAETHYLENE GLYCOL (1PEf)
03a: CALCIUM ION (CAa)
03b: CALCIUM ION (CAb)
04a: CHLORIDE ION (CLa)
05a: 1-THIOETHANESULFONIC ACID (COMa)
05b: 1-THIOETHANESULFONIC ACID (COMb)
05c: 1-THIOETHANESULFONIC ACID (COMc)
06a: THIOGLYCIN (GL3a)
06b: THIOGLYCIN (GL3b)
06c: THIOGLYCIN (GL3c)
07a: GLYCEROL (GOLa)
07b: GLYCEROL (GOLb)
08a: (17[2]S)-17[2]-METHYLTHIO-COENZYME... (M43a)
08b: (17[2]S)-17[2]-METHYLTHIO-COENZYME... (M43b)
08c: (17[2]S)-17[2]-METHYLTHIO-COENZYME... (M43c)
09a: S-OXYMETHIONINE (MHOa)
09b: S-OXYMETHIONINE (MHOb)
09c: S-OXYMETHIONINE (MHOc)
10a: N1-METHYLATED HISTIDINE (MHSa)
10b: N1-METHYLATED HISTIDINE (MHSb)
10c: N1-METHYLATED HISTIDINE (MHSc)
11a: HEXAETHYLENE GLYCOL (P6Ga)
12a: TRIETHYLENE GLYCOL (PGEa)
12b: TRIETHYLENE GLYCOL (PGEb)
12c: TRIETHYLENE GLYCOL (PGEc)
12d: TRIETHYLENE GLYCOL (PGEd)
12e: TRIETHYLENE GLYCOL (PGEe)
12f: TRIETHYLENE GLYCOL (PGEf)
13a: SULFATE ION (SO4a)
13b: SULFATE ION (SO4b)
13c: SULFATE ION (SO4c)
13d: SULFATE ION (SO4d)
13e: SULFATE ION (SO4e)
13f: SULFATE ION (SO4f)
13g: SULFATE ION (SO4g)
13h: SULFATE ION (SO4h)
13i: SULFATE ION (SO4i)
14a: COENZYME B (TP7a)
14b: COENZYME B (TP7b)
14c: COENZYME B (TP7c)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
0AF
2
Mod. Amino Acid
7-HYDROXY-L-TRYPTOPHAN
2
1PE
4
Ligand/Ion
PENTAETHYLENE GLYCOL
3
CA
-1
Ligand/Ion
CALCIUM ION
4
CL
-1
Ligand/Ion
CHLORIDE ION
5
COM
2
Ligand/Ion
1-THIOETHANESULFONIC ACID
6
GL3
2
Mod. Amino Acid
THIOGLYCIN
7
GOL
2
Ligand/Ion
GLYCEROL
8
M43
2
Ligand/Ion
(17[2]S)-17[2]-METHYLTHIO-COENZYME F43
9
MHO
2
Mod. Amino Acid
S-OXYMETHIONINE
10
MHS
2
Mod. Amino Acid
N1-METHYLATED HISTIDINE
11
P6G
1
Ligand/Ion
HEXAETHYLENE GLYCOL
12
PGE
4
Ligand/Ion
TRIETHYLENE GLYCOL
13
SO4
7
Ligand/Ion
SULFATE ION
14
TP7
2
Ligand/Ion
COENZYME B
[
close Hetero Component info
]
Sites
(27, 27)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: DC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LYS A:284 , PHE A:334 , MET A:338 , PHE A:344 , PHE A:462 , MHO A:499 , ASN A:500 , VAL A:501 , HOH A:597 , HOH A:652 , HOH A:748 , HOH A:908 , PHE B:358 , TYR B:363 , GLY B:364 , GLY B:365 , HIS B:375 , VAL B:377 , HOH B:452 , ARG D:239 , LYS D:270 , MHS D:271
BINDING SITE FOR RESIDUE TP7 A 1002
02
AC2
SOFTWARE
TYR A:347 , PHE A:462 , PHE A:463 , PHE B:357 , TYR B:363 , LEU C:117 , ARG C:120 , M43 D:1001
BINDING SITE FOR RESIDUE COM A 1003
03
AC3
SOFTWARE
ALA A:152 , VAL A:153 , ILE A:154 , GLN A:155 , MET A:158 , GLN A:244 , MET A:247 , ALA A:257 , HOH A:638 , HOH A:647 , HOH A:650 , HOH A:660 , HOH A:670 , HOH A:698 , HOH A:782 , GLY D:340 , VAL D:342 , GLY D:343 , PHE D:344 , THR D:345 , GLN D:346 , TYR D:347 , PHE D:415 , GLY D:416 , GLY D:461 , PHE D:462 , COM D:1003 , SER E:361 , ILE E:362 , TYR E:363 , LEU F:117 , SER F:118 , GLY F:119 , ARG F:153 , THR F:154 , VAL F:155 , HIS F:156 , GLY F:157 , HIS F:158 , HOH F:380
BINDING SITE FOR RESIDUE M43 A 1001
04
AC4
SOFTWARE
ARG A:239 , LYS A:270 , MHS A:271 , HOH A:612 , HOH A:615 , HOH A:668 , HOH A:680 , HOH A:716 , LYS D:284 , PHE D:334 , MET D:338 , PHE D:344 , PHE D:462 , MHO D:499 , ASN D:500 , TYR E:363 , GLY E:364 , GLY E:365 , HIS E:375 , VAL E:377
BINDING SITE FOR RESIDUE TP7 A 580
05
AC5
SOFTWARE
ASP A:16 , PHE A:18 , ALA A:19 , GLU A:20 , THR A:27 , TYR A:32 , TYR A:76 , ARG A:186 , PGE A:582 , ARG C:161 , VAL D:58 , ASN D:59
BINDING SITE FOR RESIDUE 1PE A 581
06
AC6
SOFTWARE
THR A:31 , TYR A:32 , 1PE A:581
BINDING SITE FOR RESIDUE PGE A 582
07
AC7
SOFTWARE
LYS A:38 , PRO A:79 , MET A:88 , ASN A:90 , ASN A:553 , VAL D:58
BINDING SITE FOR RESIDUE PGE A 583
08
AC8
SOFTWARE
GLU A:20 , LYS A:21 , SER A:24
BINDING SITE FOR RESIDUE SO4 A 584
09
AC9
SOFTWARE
LYS A:130 , GLU A:131
BINDING SITE FOR RESIDUE SO4 A 585
10
BC1
SOFTWARE
HIS A:121 , TYR A:140 , TYR A:253
BINDING SITE FOR RESIDUE CL A 586
11
BC2
SOFTWARE
ALA A:229 , ARG A:230 , THR A:232 , ALA D:229 , ARG D:230 , THR D:232
BINDING SITE FOR RESIDUE CA A 587
12
BC3
SOFTWARE
GLY B:166 , LYS B:171 , MET B:172 , LEU B:173 , VAL B:174 , ASP B:175 , ASN B:189 , PRO B:191 , HIS B:194 , TYR B:372 , THR B:407 , TYR B:411 , HOH B:952 , HOH B:1577 , HOH B:1691 , TYR D:267
BINDING SITE FOR RESIDUE P6G B 434
13
BC4
SOFTWARE
ALA B:48 , LYS B:107 , ARG B:108
BINDING SITE FOR RESIDUE SO4 B 435
14
BC5
SOFTWARE
ARG B:62 , HOH B:1902
BINDING SITE FOR RESIDUE SO4 B 436
15
BC6
SOFTWARE
TYR C:109 , LYS C:110
BINDING SITE FOR RESIDUE GOL C 281
16
BC7
SOFTWARE
ARG C:128 , LYS C:197 , HOH C:1497
BINDING SITE FOR RESIDUE SO4 C 282
17
BC8
SOFTWARE
GLY A:340 , GLY A:341 , VAL A:342 , GLY A:343 , PHE A:344 , THR A:345 , GLN A:346 , TYR A:347 , PHE A:415 , GLY A:416 , GLY A:461 , PHE A:462 , HOH A:661 , COM A:1003 , SER B:361 , ILE B:362 , TYR B:363 , LEU C:117 , SER C:118 , GLY C:119 , ARG C:153 , THR C:154 , VAL C:155 , HIS C:156 , GLY C:157 , HIS C:158 , HOH C:293 , ALA D:152 , VAL D:153 , ILE D:154 , GLN D:155 , GLN D:244 , MET D:247 , ALA D:257 , HOH D:593 , HOH D:615 , HOH D:635 , HOH D:641 , HOH D:688
BINDING SITE FOR RESIDUE M43 D 1001
18
BC9
SOFTWARE
M43 A:1001 , TYR D:347 , PHE D:462 , PHE D:463 , PHE E:357 , SER E:361 , TYR E:363 , LEU F:117 , ARG F:120
BINDING SITE FOR RESIDUE COM D 1003
19
CC1
SOFTWARE
ASP D:16 , PHE D:18 , ALA D:19 , GLU D:20 , TYR D:76 , ARG F:161 , VAL G:58 , ASN G:59 , ARG G:186
BINDING SITE FOR RESIDUE 1PE D 580
20
CC2
SOFTWARE
LYS D:38 , PRO D:79 , MET D:88 , ASN D:90 , ASN D:553 , HOH D:1035
BINDING SITE FOR RESIDUE PGE D 581
21
CC3
SOFTWARE
PRO D:134 , ASP D:177 , LEU D:180 , LYS D:216 , ILE D:218
BINDING SITE FOR RESIDUE PGE D 582
22
CC4
SOFTWARE
LYS D:130 , GLU D:131 , HOH D:1501
BINDING SITE FOR RESIDUE SO4 D 583
23
CC5
SOFTWARE
GLY B:68 , HOH B:1017 , LYS D:380 , ASN D:518
BINDING SITE FOR RESIDUE SO4 D 584
24
CC6
SOFTWARE
TYR A:267 , MET E:172 , ASP E:175 , PRO E:191 , HIS E:194 , VAL E:370 , TYR E:372 , THR E:407 , TYR E:411 , HOH E:1309 , HOH E:1664
BINDING SITE FOR RESIDUE 1PE E 434
25
CC7
SOFTWARE
ILE B:118 , SER B:120 , ILE E:118
BINDING SITE FOR RESIDUE GOL E 435
26
CC8
SOFTWARE
ARG F:43 , GLY F:46 , GLU F:47
BINDING SITE FOR RESIDUE 1PE F 281
27
DC3
SOFTWARE
VAL A:58 , ASN A:59 , ARG D:186 , ASP G:16 , PHE G:18 , ALA G:19 , GLU G:20 , THR G:27 , ARG I:161
BINDING SITE FOR RESIDUE 1PE G 580
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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PROSITE Patterns/Profiles
(, 0)
Info
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Exons
(0, 0)
Info
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 12)
Info
All SCOP Domains
1a: SCOP_d3sqga2 (A:284-579)
1b: SCOP_d3sqgb2 (B:184-433)
1c: SCOP_d3sqgd2 (D:284-579)
1d: SCOP_d3sqge2 (E:184-433)
1e: SCOP_d3sqgg2 (G:284-579)
1f: SCOP_d3sqgh2 (H:184-433)
2a: SCOP_d3sqga1 (A:2-283)
2b: SCOP_d3sqgb1 (B:3-183)
2c: SCOP_d3sqgd1 (D:2-283)
2d: SCOP_d3sqge1 (E:3-183)
2e: SCOP_d3sqgg1 (G:2-283)
2f: SCOP_d3sqgh1 (H:3-183)
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Classes
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Protein Domains
(
)
(
)
Organisms
(
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(
)
Class
:
All alpha proteins
(14657)
Fold
:
Methyl-coenzyme M reductase alpha and beta chain C-terminal domain
(28)
Superfamily
:
Methyl-coenzyme M reductase alpha and beta chain C-terminal domain
(28)
Family
:
automated matches
(2)
Protein domain
:
automated matches
(2)
Uncultured archaeon [TaxId: 115547]
(1)
1a
d3sqga2
A:284-579
1b
d3sqgb2
B:184-433
1c
d3sqgd2
D:284-579
1d
d3sqge2
E:184-433
1e
d3sqgg2
G:284-579
1f
d3sqgh2
H:184-433
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ferredoxin-like
(1795)
Superfamily
:
Methyl-coenzyme M reductase subunits
(42)
Family
:
automated matches
(2)
Protein domain
:
automated matches
(2)
Uncultured archaeon [TaxId: 115547]
(1)
2a
d3sqga1
A:2-283
2b
d3sqgb1
B:3-183
2c
d3sqgd1
D:2-283
2d
d3sqge1
E:3-183
2e
d3sqgg1
G:2-283
2f
d3sqgh1
H:3-183
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CATH Domains
(0, 0)
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all CATH domains
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Pfam Domains
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Asym.Unit (1.2 MB)
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Biol.Unit 1 (844 KB)
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