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3SQG
Asym. Unit
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
[
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Hetero Components
(14, 48)
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
3
Mod. Amino Acid
7-HYDROXY-L-TRYPTOPHAN
2
1PE
6
Ligand/Ion
PENTAETHYLENE GLYCOL
3
CA
2
Ligand/Ion
CALCIUM ION
4
CL
1
Ligand/Ion
CHLORIDE ION
5
COM
3
Ligand/Ion
1-THIOETHANESULFONIC ACID
6
GL3
3
Mod. Amino Acid
THIOGLYCIN
7
GOL
2
Ligand/Ion
GLYCEROL
8
M43
3
Ligand/Ion
(17[2]S)-17[2]-METHYLTHIO-COENZYME F43
9
MHO
3
Mod. Amino Acid
S-OXYMETHIONINE
10
MHS
3
Mod. Amino Acid
N1-METHYLATED HISTIDINE
11
P6G
1
Ligand/Ion
HEXAETHYLENE GLYCOL
12
PGE
6
Ligand/Ion
TRIETHYLENE GLYCOL
13
SO4
9
Ligand/Ion
SULFATE ION
14
TP7
3
Ligand/Ion
COENZYME B
[
close Hetero Component info
]
Sites
(36, 36)
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: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (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
CC9
SOFTWARE
ALA G:152 , VAL G:153 , ILE G:154 , GLN G:155 , GLN G:244 , MET G:247 , ALA G:257 , GLY G:340 , VAL G:342 , GLY G:343 , PHE G:344 , THR G:345 , GLN G:346 , TYR G:347 , PHE G:415 , GLY G:416 , GLY G:461 , PHE G:462 , HOH G:599 , HOH G:618 , HOH G:625 , HOH G:626 , HOH G:692 , HOH G:702 , HOH G:706 , HOH G:929 , COM G:1003 , SER H:361 , ILE H:362 , TYR H:363 , LEU I:117 , SER I:118 , GLY I:119 , ARG I:153 , THR I:154 , VAL I:155 , HIS I:156 , GLY I:157 , HIS I:158
BINDING SITE FOR RESIDUE M43 G 1001
28
DC1
SOFTWARE
ARG G:239 , LYS G:270 , MHS G:271 , LYS G:284 , PHE G:334 , MET G:338 , PHE G:462 , MHO G:499 , ASN G:500 , VAL G:501 , HOH G:585 , HOH G:608 , HOH G:1225 , HOH G:1251 , HOH G:1985 , TYR H:363 , GLY H:364 , GLY H:365 , HIS H:375 , VAL H:377 , HOH H:902
BINDING SITE FOR RESIDUE TP7 G 1002
29
DC2
SOFTWARE
TYR G:347 , PHE G:462 , PHE G:463 , M43 G:1001 , PHE H:357 , SER H:361 , TYR H:363 , HOH H:1344 , LEU I:117 , ARG I:120
BINDING SITE FOR RESIDUE COM G 1003
30
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
31
DC4
SOFTWARE
LYS G:38 , MET G:88 , ASN G:90 , ASN G:553 , HOH G:1266 , HOH G:1357
BINDING SITE FOR RESIDUE PGE G 581
32
DC5
SOFTWARE
THR G:31 , TYR G:32 , HOH G:1736
BINDING SITE FOR RESIDUE PGE G 582
33
DC6
SOFTWARE
ALA G:229 , ARG G:230 , THR G:232
BINDING SITE FOR RESIDUE CA G 583
34
DC7
SOFTWARE
TYR G:267 , HOH G:751 , LYS H:171 , MET H:172 , LEU H:173 , VAL H:174 , ASP H:175 , ASN H:189 , PRO H:191 , HIS H:194 , TYR H:372 , TYR H:411 , HOH H:1900
BINDING SITE FOR RESIDUE 1PE H 434
35
DC8
SOFTWARE
ARG H:62
BINDING SITE FOR RESIDUE SO4 H 435
36
DC9
SOFTWARE
ARG I:276 , HOH I:1117
BINDING SITE FOR RESIDUE SO4 I 281
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
[
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
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End label:
Sorry, no Info available
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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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Protein Domains
(
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(
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Organisms
(
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(
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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
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
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Pfam Domains
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all PFAM domains
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