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1E6Y
Asym. Unit
Info
Asym.Unit (433 KB)
Biol.Unit 1 (424 KB)
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(1)
Title
:
METHYL-COENZYME M REDUCTASE FROM METHANOSARCINA BARKERI
Authors
:
W. Grabarse, U. Ermler
Date
:
23 Aug 00 (Deposition) - 18 Oct 00 (Release) - 29 Mar 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.60
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Biological Methanogenesis, Ni-Enzyme, Oxidoreductase, Ni Enzyme
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
W. Grabarse, F. Mahlert, S. Shima, R. K. Thauer, U. Ermler
Comparison Of Three Methyl-Coenzyme M Reductases From Phylogenetically Distant Organisms: Unusual Amino Acid Modification, Conservation And Adaptation
J. Mol. Biol. V. 303 329 2000
[
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Hetero Components
(9, 19)
Info
All Hetero Components
1a: 5-METHYL-ARGININE (AGMa)
1b: 5-METHYL-ARGININE (AGMb)
2a: 1-THIOETHANESULFONIC ACID (COMa)
2b: 1-THIOETHANESULFONIC ACID (COMb)
3a: FACTOR 430 (F43a)
3b: FACTOR 430 (F43b)
4a: THIOGLYCIN (GL3a)
4b: THIOGLYCIN (GL3b)
5a: GLYCEROL (GOLa)
5b: GLYCEROL (GOLb)
5c: GLYCEROL (GOLc)
6a: N1-METHYLATED HISTIDINE (MHSa)
6b: N1-METHYLATED HISTIDINE (MHSb)
7a: CYSTEINESULFONIC ACID (OCSa)
7b: CYSTEINESULFONIC ACID (OCSb)
8a: S-METHYLCYSTEINE (SMCa)
8b: S-METHYLCYSTEINE (SMCb)
9a: COENZYME B (TP7a)
9b: COENZYME B (TP7b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
AGM
2
Mod. Amino Acid
5-METHYL-ARGININE
2
COM
2
Ligand/Ion
1-THIOETHANESULFONIC ACID
3
F43
2
Ligand/Ion
FACTOR 430
4
GL3
2
Mod. Amino Acid
THIOGLYCIN
5
GOL
3
Ligand/Ion
GLYCEROL
6
MHS
2
Mod. Amino Acid
N1-METHYLATED HISTIDINE
7
OCS
2
Mod. Amino Acid
CYSTEINESULFONIC ACID
8
SMC
2
Mod. Amino Acid
S-METHYLCYSTEINE
9
TP7
2
Ligand/Ion
COENZYME B
[
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]
Sites
(9, 9)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
9: AC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ALA A:1158 , VAL A:1159 , VAL A:1160 , GLN A:1161 , GLN A:1244 , MET A:1247 , ALA A:1257 , HOH A:2224 , HOH A:2477 , HOH A:2478 , HOH A:2479 , HOH A:2480 , HOH A:2481 , HOH D:2427 , GLY D:4339 , GLY D:4340 , VAL D:4341 , GLY D:4342 , PHE D:4343 , THR D:4344 , GLN D:4345 , TYR D:4346 , PHE D:4416 , GLY D:4417 , GLY D:4462 , PHE D:4463 , COM D:5572 , SER E:5363 , ILE E:5364 , TYR E:5365 , LEU F:6118 , SER F:6119 , GLY F:6120 , ALA F:6154 , THR F:6155 , VAL F:6156 , HIS F:6157 , HIS F:6159
BINDING SITE FOR RESIDUE F43 A 2570
2
AC2
SOFTWARE
ARG A:1284 , LEU A:1333 , MET A:1337 , SER A:1338 , PHE A:1343 , PHE A:1463 , MET A:1500 , ASN A:1501 , VAL A:1502 , HOH A:2275 , HOH A:2482 , HOH A:2483 , HOH A:2484 , HOH A:2485 , HOH A:2486 , PHE B:2360 , TYR B:2365 , GLY B:2367 , HIS B:2377 , VAL B:2378 , ARG D:4239 , LYS D:4270 , MHS D:4271
BINDING SITE FOR RESIDUE TP7 A 2571
3
AC3
SOFTWARE
TYR A:1346 , PHE A:1463 , PHE A:1464 , HOH A:2487 , PHE B:2359 , TYR B:2365 , LEU C:3118 , ARG C:3121 , F43 D:5570
BINDING SITE FOR RESIDUE COM A 2572
4
AC4
SOFTWARE
GLY A:1339 , GLY A:1340 , VAL A:1341 , GLY A:1342 , PHE A:1343 , THR A:1344 , GLN A:1345 , TYR A:1346 , PHE A:1416 , GLY A:1417 , GLY A:1462 , PHE A:1463 , HOH A:2353 , COM A:2572 , SER B:2363 , ILE B:2364 , TYR B:2365 , LEU C:3118 , SER C:3119 , GLY C:3120 , ALA C:3154 , THR C:3155 , VAL C:3156 , HIS C:3157 , HIS C:3159 , HOH D:2285 , HOH D:2511 , HOH D:2512 , HOH D:2513 , HOH D:2514 , HOH D:2515 , ALA D:4158 , VAL D:4159 , VAL D:4160 , GLN D:4161 , GLN D:4244 , MET D:4247 , ALA D:4257
BINDING SITE FOR RESIDUE F43 D 5570
5
AC5
SOFTWARE
ARG A:1239 , LYS A:1270 , MHS A:1271 , HOH D:2366 , HOH D:2461 , HOH D:2517 , HOH D:2518 , HOH D:2519 , HOH D:2520 , ARG D:4284 , LEU D:4333 , MET D:4337 , SER D:4338 , PHE D:4463 , MET D:4500 , ASN D:4501 , VAL D:4502 , PHE E:5360 , TYR E:5365 , GLY E:5367 , HIS E:5377 , VAL E:5378
BINDING SITE FOR RESIDUE TP7 D 5571
6
AC6
SOFTWARE
F43 A:2570 , HOH D:2521 , TYR D:4346 , PHE D:4463 , PHE D:4464 , PHE E:5359 , TYR E:5365 , LEU F:6118 , ARG F:6121
BINDING SITE FOR RESIDUE COM D 5572
7
AC7
SOFTWARE
LYS A:1379 , LYS A:1382 , THR A:1437 , GLY A:1438 , ARG A:1519 , HOH A:2362 , HOH A:2488 , GLY E:5068
BINDING SITE FOR RESIDUE GOL A 2573
8
AC8
SOFTWARE
MHS A:1271 , LEU A:1274 , VAL A:1275 , SER A:1276 , GLU A:1279 , HOH A:2489 , LYS E:5062 , MET E:5168
BINDING SITE FOR RESIDUE GOL A 2574
9
AC9
SOFTWARE
GLY B:2068 , ARG B:2069 , HOH D:2522 , LYS D:4379 , LYS D:4382 , THR D:4437 , GLY D:4438 , ARG D:4519
BINDING SITE FOR RESIDUE GOL D 5573
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
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Sorry, no Info available
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Exons
(0, 0)
Info
All Exons
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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
(5, 10)
Info
All SCOP Domains
1a: SCOP_d1e6ya1 (A:1284-1569)
1b: SCOP_d1e6yd1 (D:4284-4569)
2a: SCOP_d1e6yb1 (B:2186-2433)
2b: SCOP_d1e6ye1 (E:5186-5434)
3a: SCOP_d1e6ya2 (A:1002-1283)
3b: SCOP_d1e6yd2 (D:4002-4283)
4a: SCOP_d1e6yb2 (B:2002-2185)
4b: SCOP_d1e6ye2 (E:5002-5185)
5a: SCOP_d1e6yc_ (C:)
5b: SCOP_d1e6yf_ (F:)
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)
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(
)
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(
)
(
)
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(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
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
:
Methyl-coenzyme M reductase alpha and beta chain C-terminal domain
(26)
Protein domain
:
Alpha chain
(13)
Methanosarcina barkeri [TaxId: 2208]
(1)
1a
d1e6ya1
A:1284-1569
1b
d1e6yd1
D:4284-4569
Protein domain
:
Beta chain
(13)
Methanosarcina barkeri [TaxId: 2208]
(1)
2a
d1e6yb1
B:2186-2433
2b
d1e6ye1
E:5186-5434
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ferredoxin-like
(1795)
Superfamily
:
Methyl-coenzyme M reductase subunits
(42)
Family
:
Methyl-coenzyme M reductase alpha and beta chain N-terminal domain
(26)
Protein domain
:
Alpha chain
(13)
Methanosarcina barkeri [TaxId: 2208]
(1)
3a
d1e6ya2
A:1002-1283
3b
d1e6yd2
D:4002-4283
Protein domain
:
Beta chain
(13)
Methanosarcina barkeri [TaxId: 2208]
(1)
4a
d1e6yb2
B:2002-2185
4b
d1e6ye2
E:5002-5185
Family
:
Methyl-coenzyme M reductase gamma chain
(14)
Protein domain
:
Methyl-coenzyme M reductase gamma chain
(14)
Methanosarcina barkeri [TaxId: 2208]
(1)
5a
d1e6yc_
C:
5b
d1e6yf_
F:
[
close SCOP info
]
CATH Domains
(4, 12)
Info
all CATH domains
1a: CATH_1e6yA02 (A:1116-1290)
1b: CATH_1e6yD02 (D:4116-4290)
1c: CATH_1e6yB01 (B:2042-2188)
1d: CATH_1e6yE01 (E:5042-5188)
2a: CATH_1e6yC00 (C:3002-3248)
2b: CATH_1e6yF00 (F:6002-6248)
3a: CATH_1e6yA01 (A:1006-1115)
3b: CATH_1e6yD01 (D:4006-4115)
4a: CATH_1e6yA03 (A:1291-1526)
4b: CATH_1e6yD03 (D:4291-4526)
4c: CATH_1e6yB02 (B:2002-2041,B:2189-2433)
4d: CATH_1e6yE02 (E:5002-5041,E:5189-5434)
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)
(
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Architectures
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)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Alpha-Beta Plaits
(1688)
Homologous Superfamily
:
[code=3.30.70.470, no name defined]
(7)
Methanosarcina barkeri. Organism_taxid: 2208.
(1)
1a
1e6yA02
A:1116-1290
1b
1e6yD02
D:4116-4290
1c
1e6yB01
B:2042-2188
1d
1e6yE01
E:5042-5188
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Lambda Exonuclease; Chain A
(10)
Homologous Superfamily
:
[code=3.90.320.20, no name defined]
(7)
Methanosarcina barkeri. Organism_taxid: 2208.
(1)
2a
1e6yC00
C:3002-3248
2b
1e6yF00
F:6002-6248
Topology
:
Methyl-coenzyme M Reductase; Chain A, domain 1
(7)
Homologous Superfamily
:
Methyl-coenzyme M Reductase; Chain A, domain 1
(7)
Methanosarcina barkeri. Organism_taxid: 2208.
(1)
3a
1e6yA01
A:1006-1115
3b
1e6yD01
D:4006-4115
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Methyl-coenzyme M Reductase; Chain B, domain 2
(7)
Homologous Superfamily
:
Methyl-coenzyme M Reductase; Chain B, domain 2
(7)
Methanosarcina barkeri. Organism_taxid: 2208.
(1)
4a
1e6yA03
A:1291-1526
4b
1e6yD03
D:4291-4526
4c
1e6yB02
B:2002-2041,B:2189-2433
4d
1e6yE02
E:5002-5041,E:5189-5434
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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Asym.Unit (433 KB)
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