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1HBM
Asym. Unit
Info
Asym.Unit (447 KB)
Biol.Unit 1 (435 KB)
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(1)
Title
:
METHYL-COENZYME M REDUCTASE ENZYME PRODUCT COMPLEX
Authors
:
U. Ermler, W. Grabarse
Date
:
20 Apr 01 (Deposition) - 16 Aug 01 (Release) - 29 Mar 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Methanogenesis, Biological Methanogenesis, Ni-Enzyme, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
W. Grabarse, F. Mahlert, E. C. Duin, M. Goubeaud, S. Shima, R. K. Thauer V. Lamzin, U. Ermler
On The Mechanism Of Biological Methane Formation: Structura Evidence For Conformational Changes In Methyl-Coenzyme M Reductase Upon Substrate Binding
J. Mol. Biol. V. 309 315 2001
[
close entry info
]
Hetero Components
(12, 42)
Info
All Hetero Components
01a: 5-METHYL-ARGININE (AGMa)
01b: 5-METHYL-ARGININE (AGMb)
02a: CHLORIDE ION (CLa)
02b: CHLORIDE ION (CLb)
03a: FACTOR 430 (F43a)
03b: FACTOR 430 (F43b)
04a: THIOGLYCIN (GL3a)
04b: THIOGLYCIN (GL3b)
05a: GLYCEROL (GOLa)
05b: GLYCEROL (GOLb)
05c: GLYCEROL (GOLc)
05d: GLYCEROL (GOLd)
05e: GLYCEROL (GOLe)
05f: GLYCEROL (GOLf)
05g: GLYCEROL (GOLg)
05h: GLYCEROL (GOLh)
05i: GLYCEROL (GOLi)
05j: GLYCEROL (GOLj)
05k: GLYCEROL (GOLk)
07a: 2-METHYL-GLUTAMINE (MGNa)
07b: 2-METHYL-GLUTAMINE (MGNb)
06a: MAGNESIUM ION (MGa)
06b: MAGNESIUM ION (MGb)
06c: MAGNESIUM ION (MGc)
06d: MAGNESIUM ION (MGd)
06e: MAGNESIUM ION (MGe)
08a: N1-METHYLATED HISTIDINE (MHSa)
08b: N1-METHYLATED HISTIDINE (MHSb)
09a: SODIUM ION (NAa)
09b: SODIUM ION (NAb)
09c: SODIUM ION (NAc)
09d: SODIUM ION (NAd)
09e: SODIUM ION (NAe)
09f: SODIUM ION (NAf)
09g: SODIUM ION (NAg)
09h: SODIUM ION (NAh)
09i: SODIUM ION (NAi)
10a: O-PHOSPHONO-N-{(2E)-7-[(2-SULFOETH... (SHTa)
10b: O-PHOSPHONO-N-{(2E)-7-[(2-SULFOETH... (SHTb)
11a: S-METHYLCYSTEINE (SMCa)
11b: S-METHYLCYSTEINE (SMCb)
12a: ZINC ION (ZNa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
AGM
2
Mod. Amino Acid
5-METHYL-ARGININE
2
CL
2
Ligand/Ion
CHLORIDE ION
3
F43
2
Ligand/Ion
FACTOR 430
4
GL3
2
Mod. Amino Acid
THIOGLYCIN
5
GOL
11
Ligand/Ion
GLYCEROL
6
MG
5
Ligand/Ion
MAGNESIUM ION
7
MGN
2
Mod. Amino Acid
2-METHYL-GLUTAMINE
8
MHS
2
Mod. Amino Acid
N1-METHYLATED HISTIDINE
9
NA
9
Ligand/Ion
SODIUM ION
10
SHT
2
Ligand/Ion
O-PHOSPHONO-N-{(2E)-7-[(2-SULFOETHYL)DITHIO]HEPT-2-ENOYL}-L-THREONINE
11
SMC
2
Mod. Amino Acid
S-METHYLCYSTEINE
12
ZN
1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(32, 32)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LYS A:11 , PHE A:14 , HOH A:2027 , HOH A:2035 , HOH A:2036 , HOH A:2044
BINDING SITE FOR RESIDUE NA A1556
02
AC2
SOFTWARE
ARG A:270 , HOH A:2261 , HOH A:2420 , GOL D:1553 , HOH D:2437
BINDING SITE FOR RESIDUE NA A1557
03
AC3
SOFTWARE
ALA A:544 , THR A:547 , PRO A:548 , HOH A:2407 , HOH A:2410
BINDING SITE FOR RESIDUE NA A1558
04
AC4
SOFTWARE
PRO A:58 , ILE A:60 , THR A:62 , HOH A:2110 , HOH A:2113 , HOH D:2172
BINDING SITE FOR RESIDUE NA A1559
05
AC5
SOFTWARE
HOH A:2102 , ASN B:441 , HOH B:2368 , HOH D:2197 , HOH D:2198
BINDING SITE FOR RESIDUE NA B1445
06
AC6
SOFTWARE
ARG B:235 , HOH B:2109 , HOH B:2248
BINDING SITE FOR RESIDUE CL B1446
07
AC7
SOFTWARE
ASP B:99 , THR B:101 , HOH B:2122 , HOH B:2140 , HOH B:2145 , HOH B:2147
BINDING SITE FOR RESIDUE NA B1447
08
AC8
SOFTWARE
GLU C:30 , HOH C:2027 , HOH C:2055 , HOH C:2058 , HOH C:2152 , HOH F:2040
BINDING SITE FOR RESIDUE MG C1250
09
AC9
SOFTWARE
ARG A:102 , SER A:215 , ARG A:216 , CYS A:218 , ARG D:102 , SER D:215 , ARG D:216 , CYS D:218
BINDING SITE FOR RESIDUE ZN D1556
10
BC1
SOFTWARE
LYS D:11 , PHE D:14 , HOH D:2016 , HOH D:2017 , HOH D:2022 , HOH D:2028
BINDING SITE FOR RESIDUE NA D1557
11
BC2
SOFTWARE
GOL A:1552 , ARG D:270 , HOH D:2139 , HOH D:2266 , HOH D:2432
BINDING SITE FOR RESIDUE NA D1558
12
BC3
SOFTWARE
HOH A:2174 , PRO D:58 , ILE D:60 , THR D:62 , HOH D:2098 , HOH D:2103
BINDING SITE FOR RESIDUE NA D1559
13
BC4
SOFTWARE
ARG E:235
BINDING SITE FOR RESIDUE CL E1445
14
BC5
SOFTWARE
HOH C:2050 , GLU F:30 , HOH F:2018 , HOH F:2044 , HOH F:2048 , HOH F:2143
BINDING SITE FOR RESIDUE MG F1249
15
BC6
SOFTWARE
HOH E:2036 , HOH E:2037 , HOH E:2100 , HOH E:2101
BINDING SITE FOR RESIDUE MG F1250
16
BC7
SOFTWARE
HOH A:2018 , HOH A:2019 , HOH A:2021 , HOH A:2040 , HOH A:2058
BINDING SITE FOR RESIDUE MG F1251
17
BC8
SOFTWARE
HOH A:2025 , HOH A:2053 , HOH A:2330
BINDING SITE FOR RESIDUE MG F1252
18
BC9
SOFTWARE
GLY A:326 , GLY A:327 , VAL A:328 , GLY A:329 , PHE A:330 , THR A:331 , GLN A:332 , TYR A:333 , GLY A:397 , GLY A:442 , PHE A:443 , SHT A:1551 , HOH A:2334 , HOH A:2413 , HOH A:2414 , HOH A:2415 , HOH A:2416 , HOH A:2417 , SER B:365 , ILE B:366 , TYR B:367 , LEU C:117 , SER C:118 , GLY C:119 , LYS C:153 , SER C:154 , VAL C:155 , HIS C:156 , HIS C:158 , HOH C:2126 , HOH C:2160 , ALA D:144 , VAL D:145 , VAL D:146 , GLN D:147 , GLN D:230 , MET D:233 , ALA D:243
BINDING SITE FOR RESIDUE F43 A1550
19
CC1
SOFTWARE
ARG A:270 , LEU A:320 , MET A:324 , SER A:325 , PHE A:330 , TYR A:333 , PHE A:443 , MET A:480 , VAL A:482 , F43 A:1550 , HOH A:2418 , HOH A:2419 , HOH A:2420 , HOH A:2421 , HOH A:2422 , HOH A:2423 , TYR B:367 , GLY B:368 , GLY B:369 , HIS B:379 , ILE B:380 , ARG D:225 , LYS D:256 , MHS D:257
BINDING SITE FOR RESIDUE SHT A1551
20
CC2
SOFTWARE
ALA A:144 , VAL A:145 , VAL A:146 , GLN A:147 , GLN A:230 , MET A:233 , ALA A:243 , HOH A:2176 , HOH A:2235 , GLY D:326 , GLY D:327 , VAL D:328 , GLY D:329 , PHE D:330 , THR D:331 , GLN D:332 , TYR D:333 , GLY D:397 , GLY D:442 , PHE D:443 , SHT D:1551 , HOH D:2425 , HOH D:2426 , HOH D:2427 , HOH D:2428 , HOH D:2429 , SER E:365 , ILE E:366 , TYR E:367 , LEU F:117 , SER F:118 , GLY F:119 , LYS F:153 , SER F:154 , VAL F:155 , HIS F:156 , HIS F:158 , HOH F:2153
BINDING SITE FOR RESIDUE F43 D1550
21
CC3
SOFTWARE
ARG A:225 , LYS A:256 , MHS A:257 , ARG D:270 , LEU D:320 , MET D:324 , PHE D:330 , TYR D:333 , PHE D:443 , MET D:480 , VAL D:482 , F43 D:1550 , HOH D:2430 , HOH D:2431 , HOH D:2432 , HOH D:2433 , HOH D:2434 , HOH D:2435 , TYR E:367 , GLY E:369 , HIS E:379 , ILE E:380
BINDING SITE FOR RESIDUE SHT D1551
22
CC4
SOFTWARE
SER A:224 , LYS A:256 , HIS A:262 , GLU A:275 , HOH A:2424 , NA D:1558 , HOH D:2266 , HOH D:2432
BINDING SITE FOR RESIDUE GOL A1552
23
CC5
SOFTWARE
ASP A:170 , ALA A:173 , ASP A:174 , ASP A:183 , ASN A:185 , HOH A:2425 , HOH A:2426
BINDING SITE FOR RESIDUE GOL A1553
24
CC6
SOFTWARE
VAL A:519 , LYS A:531 , PHE A:537 , GLU A:538 , HOH A:2382 , HOH A:2392 , HOH A:2393
BINDING SITE FOR RESIDUE GOL A1554
25
CC7
SOFTWARE
LYS A:4 , ASP A:345 , TYR A:348 , GLU A:352 , TYR A:380 , HOH A:2008
BINDING SITE FOR RESIDUE GOL A1555
26
CC8
SOFTWARE
LYS B:3 , GLU B:25 , SER B:28 , ARG B:31 , GLU B:234 , HOH B:2250 , HOH B:2369 , VAL E:95
BINDING SITE FOR RESIDUE GOL B1444
27
CC9
SOFTWARE
TYR C:109 , ARG C:110 , ASP C:129 , HOH C:2134 , HOH C:2255 , HOH C:2256 , HOH C:2257
BINDING SITE FOR RESIDUE GOL C1249
28
DC1
SOFTWARE
ASP D:170 , ALA D:173 , ASP D:174 , ASP D:183 , ASN D:185 , HOH D:2203 , HOH D:2204 , HOH D:2436
BINDING SITE FOR RESIDUE GOL D1552
29
DC2
SOFTWARE
NA A:1557 , HOH A:2420 , SER D:224 , LYS D:256 , MHS D:257 , HIS D:262 , GLU D:275
BINDING SITE FOR RESIDUE GOL D1553
30
DC3
SOFTWARE
GLN D:291 , ARG D:294 , PHE D:513 , ASP D:515 , ASP D:516 , PHE D:520 , ASP D:521 , PHE D:522 , THR D:523
BINDING SITE FOR RESIDUE GOL D1554
31
DC4
SOFTWARE
ASP D:345 , TYR D:348 , GLU D:352 , TYR D:380
BINDING SITE FOR RESIDUE GOL D1555
32
DC5
SOFTWARE
VAL B:95 , LYS E:3 , GLU E:25 , SER E:28 , ARG E:31 , GLU E:234 , HOH E:2353
BINDING SITE FOR RESIDUE GOL E1444
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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[
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
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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
View:
Label:
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_d1hbma1 (A:270-549)
1b: SCOP_d1hbmd1 (D:270-549)
2a: SCOP_d1hbmb1 (B:189-443)
2b: SCOP_d1hbme1 (E:189-443)
3a: SCOP_d1hbma2 (A:2-269)
3b: SCOP_d1hbmd2 (D:2-269)
4a: SCOP_d1hbmb2 (B:2-188)
4b: SCOP_d1hbme2 (E:2-188)
5a: SCOP_d1hbmc_ (C:)
5b: SCOP_d1hbmf_ (F:)
View:
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)
(
)
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(
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(
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)
(
)
Families
(
)
(
)
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)
Methanobacterium thermoautotrophicum [TaxId: 145262]
(11)
1a
d1hbma1
A:270-549
1b
d1hbmd1
D:270-549
Protein domain
:
Beta chain
(13)
Methanobacterium thermoautotrophicum [TaxId: 145262]
(11)
2a
d1hbmb1
B:189-443
2b
d1hbme1
E:189-443
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)
Methanobacterium thermoautotrophicum [TaxId: 145262]
(11)
3a
d1hbma2
A:2-269
3b
d1hbmd2
D:2-269
Protein domain
:
Beta chain
(13)
Methanobacterium thermoautotrophicum [TaxId: 145262]
(11)
4a
d1hbmb2
B:2-188
4b
d1hbme2
E:2-188
Family
:
Methyl-coenzyme M reductase gamma chain
(14)
Protein domain
:
Methyl-coenzyme M reductase gamma chain
(14)
Methanobacterium thermoautotrophicum [TaxId: 145262]
(12)
5a
d1hbmc_
C:
5b
d1hbmf_
F:
[
close SCOP info
]
CATH Domains
(4, 12)
Info
all CATH domains
1a: CATH_1hbmA02 (A:102-276)
1b: CATH_1hbmB01 (B:45-191)
1c: CATH_1hbmE01 (E:45-191)
1d: CATH_1hbmD02 (D:102-276)
2a: CATH_1hbmC00 (C:2-248)
2b: CATH_1hbmF00 (F:2-248)
3a: CATH_1hbmA01 (A:3-101)
3b: CATH_1hbmD01 (D:3-101)
4a: CATH_1hbmA03 (A:277-536)
4b: CATH_1hbmB02 (B:2-44,B:192-443)
4c: CATH_1hbmE02 (E:2-44,E:192-443)
4d: CATH_1hbmD03 (D:277-536)
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Homologous Superfamilies
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)
(
)
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)
Methanothermobacter thermautotrophicus. Organism_taxid: 145262. Strain: marburg.
(3)
1a
1hbmA02
A:102-276
1b
1hbmB01
B:45-191
1c
1hbmE01
E:45-191
1d
1hbmD02
D:102-276
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Lambda Exonuclease; Chain A
(10)
Homologous Superfamily
:
[code=3.90.320.20, no name defined]
(7)
Methanothermobacter thermautotrophicus. Organism_taxid: 145262. Strain: marburg.
(3)
2a
1hbmC00
C:2-248
2b
1hbmF00
F:2-248
Topology
:
Methyl-coenzyme M Reductase; Chain A, domain 1
(7)
Homologous Superfamily
:
Methyl-coenzyme M Reductase; Chain A, domain 1
(7)
Methanothermobacter thermautotrophicus. Organism_taxid: 145262. Strain: marburg.
(3)
3a
1hbmA01
A:3-101
3b
1hbmD01
D:3-101
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)
Methanothermobacter thermautotrophicus. Organism_taxid: 145262. Strain: marburg.
(3)
4a
1hbmA03
A:277-536
4b
1hbmB02
B:2-44,B:192-443
4c
1hbmE02
E:2-44,E:192-443
4d
1hbmD03
D:277-536
[
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]
Pfam Domains
(0, 0)
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all PFAM domains
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