PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
3M2U
Asym. Unit
Info
Asym.Unit (467 KB)
Biol.Unit 1 (455 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURAL INSIGHT INTO METHYL-COENZYME M REDUCTASE CHEMISTRY USING COENZYME B ANALOGUES
Authors
:
P. E. Cedervall, M. Dey, S. W. Ragsdale, C. M. Wilmot
Date
:
08 Mar 10 (Deposition) - 15 Sep 10 (Release) - 29 Mar 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.40
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Methyl-Coenzyme M Reductase, Nickel, Metal-Binding, Methanogenesis, Methylation, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. E. Cedervall, M. Dey, A. R. Pearson, S. W. Ragsdale, C. M. Wilmot
Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues.
Biochemistry V. 49 7683 2010
[
close entry info
]
Hetero Components
(14, 41)
Info
All Hetero Components
01a: ACETATE ION (ACTa)
01b: ACETATE ION (ACTb)
02a: 5-METHYL-ARGININE (AGMa)
02b: 5-METHYL-ARGININE (AGMb)
03a: 1-THIOETHANESULFONIC ACID (COMa)
03b: 1-THIOETHANESULFONIC ACID (COMb)
04a: 1,2-ETHANEDIOL (EDOa)
04b: 1,2-ETHANEDIOL (EDOb)
04c: 1,2-ETHANEDIOL (EDOc)
04d: 1,2-ETHANEDIOL (EDOd)
04e: 1,2-ETHANEDIOL (EDOe)
04f: 1,2-ETHANEDIOL (EDOf)
04g: 1,2-ETHANEDIOL (EDOg)
05a: FACTOR 430 (F43a)
05b: FACTOR 430 (F43b)
06a: THIOGLYCIN (GL3a)
06b: THIOGLYCIN (GL3b)
08a: 2-METHYL-GLUTAMINE (MGNa)
08b: 2-METHYL-GLUTAMINE (MGNb)
07a: MAGNESIUM ION (MGa)
07b: MAGNESIUM ION (MGb)
07c: MAGNESIUM ION (MGc)
07d: MAGNESIUM ION (MGd)
07e: MAGNESIUM ION (MGe)
07f: MAGNESIUM ION (MGf)
07g: MAGNESIUM ION (MGg)
07h: MAGNESIUM ION (MGh)
07i: MAGNESIUM ION (MGi)
07j: MAGNESIUM ION (MGj)
07k: MAGNESIUM ION (MGk)
09a: N1-METHYLATED HISTIDINE (MHSa)
09b: N1-METHYLATED HISTIDINE (MHSb)
10a: DI(HYDROXYETHYL)ETHER (PEGa)
10b: DI(HYDROXYETHYL)ETHER (PEGb)
11a: S-METHYLCYSTEINE (SMCa)
11b: S-METHYLCYSTEINE (SMCb)
12a: COENZYME B (TP7a)
12b: COENZYME B (TP7b)
13a: O-PHOSPHONO-N-(6-SULFANYLHEXANOYL)... (TXZa)
13b: O-PHOSPHONO-N-(6-SULFANYLHEXANOYL)... (TXZb)
14a: ZINC ION (ZNa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
2
Ligand/Ion
ACETATE ION
2
AGM
2
Mod. Amino Acid
5-METHYL-ARGININE
3
COM
2
Ligand/Ion
1-THIOETHANESULFONIC ACID
4
EDO
7
Ligand/Ion
1,2-ETHANEDIOL
5
F43
2
Ligand/Ion
FACTOR 430
6
GL3
2
Mod. Amino Acid
THIOGLYCIN
7
MG
11
Ligand/Ion
MAGNESIUM ION
8
MGN
2
Mod. Amino Acid
2-METHYL-GLUTAMINE
9
MHS
2
Mod. Amino Acid
N1-METHYLATED HISTIDINE
10
PEG
2
Ligand/Ion
DI(HYDROXYETHYL)ETHER
11
SMC
2
Mod. Amino Acid
S-METHYLCYSTEINE
12
TP7
2
Ligand/Ion
COENZYME B
13
TXZ
2
Ligand/Ion
O-PHOSPHONO-N-(6-SULFANYLHEXANOYL)-L-THREONINE
14
ZN
1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(31, 31)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ACT A:556 , HOH A:713 , HOH A:1599 , HOH A:2285 , HOH A:3828 , HOH A:3971
BINDING SITE FOR RESIDUE MG A 551
02
AC2
SOFTWARE
GLU A:20 , HOH A:657 , HOH A:1164 , HOH A:3761 , HOH A:4216 , HOH A:4217
BINDING SITE FOR RESIDUE MG A 552
03
AC3
SOFTWARE
ALA A:144 , VAL A:145 , VAL A:146 , GLN A:147 , GLN A:230 , MET A:233 , ALA A:243 , HOH A:652 , HOH A:675 , HOH A:677 , HOH A:697 , HOH A:699 , HOH A:788 , HOH A:4193 , GLY D:326 , GLY D:327 , VAL D:328 , GLY D:329 , PHE D:330 , THR D:331 , GLN D:332 , TYR D:333 , PHE D:396 , GLY D:397 , GLY D:442 , PHE D:443 , COM D:555 , HOH D:666 , 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:582
BINDING SITE FOR RESIDUE F43 A 1
04
AC4
SOFTWARE
ARG A:270 , LEU A:320 , MET A:324 , SER A:325 , PHE A:443 , MET A:480 , ASN A:481 , VAL A:482 , HOH A:592 , HOH A:607 , HOH A:621 , HOH A:685 , HOH A:3684 , PHE B:362 , 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 TP7 A 553
05
AC5
SOFTWARE
TYR A:333 , PHE A:443 , TYR A:444 , HOH A:3682 , HOH A:4190 , HOH A:4191 , HOH A:4192 , HOH A:4194 , PHE B:361 , SER B:365 , TYR B:367 , LEU C:117 , ARG C:120 , F43 D:553
BINDING SITE FOR RESIDUE COM A 554
06
AC6
SOFTWARE
ARG A:270 , MET A:324 , PHE A:443 , MET A:480 , ASN A:481 , VAL A:482 , HOH A:592 , HOH A:607 , HOH A:621 , HOH A:685 , HOH A:3684 , PHE B:362 , 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 TXZ A 555
07
AC7
SOFTWARE
VAL A:519 , LYS A:531 , PHE A:537 , GLU A:538 , MG A:551 , HOH A:642 , HOH A:713 , HOH A:1396 , HOH A:2285 , HOH A:3828 , HOH A:3971 , HOH A:3988
BINDING SITE FOR RESIDUE ACT A 556
08
AC8
SOFTWARE
TYR A:348
BINDING SITE FOR RESIDUE EDO A 557
09
AC9
SOFTWARE
ASN A:110 , HIS A:111
BINDING SITE FOR RESIDUE EDO A 558
10
BC1
SOFTWARE
ALA A:48 , HOH A:4212 , LYS B:7
BINDING SITE FOR RESIDUE PEG A 559
11
BC2
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 A 560
12
BC3
SOFTWARE
HOH B:1305 , HOH B:3547 , HOH B:3548 , HOH B:3549 , HOH B:3550 , HOH B:3714
BINDING SITE FOR RESIDUE MG B 444
13
BC4
SOFTWARE
ASP B:271 , HOH B:564 , HOH B:811 , HOH B:1206 , HOH B:3076 , HOH B:4127
BINDING SITE FOR RESIDUE MG B 445
14
BC5
SOFTWARE
GLU C:30 , HOH C:1095 , HOH C:3555 , HOH C:3556 , HOH C:3557 , HOH C:3558
BINDING SITE FOR RESIDUE MG C 250
15
BC6
SOFTWARE
LYS C:153 , HOH C:1067
BINDING SITE FOR RESIDUE ACT C 1
16
BC7
SOFTWARE
ARG C:236 , HOH C:856 , HOH C:3762
BINDING SITE FOR RESIDUE EDO C 251
17
BC8
SOFTWARE
ARG C:43 , GLY C:46 , GLU C:47 , GLU C:48 , TYR C:49 , HOH C:3630
BINDING SITE FOR RESIDUE PEG C 252
18
BC9
SOFTWARE
HOH D:3543 , HOH D:3544 , HOH D:3546 , HOH F:3542 , HOH F:3545
BINDING SITE FOR RESIDUE MG D 1
19
CC1
SOFTWARE
HOH D:1116 , HOH D:3559 , HOH D:3560 , HOH D:3561 , HOH D:3562 , HOH D:3563
BINDING SITE FOR RESIDUE MG D 551
20
CC2
SOFTWARE
GLU D:175 , HOH D:4000 , HOH D:4001 , HOH D:4183
BINDING SITE FOR RESIDUE MG D 552
21
CC3
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 , PHE A:396 , GLY A:397 , GLY A:442 , PHE A:443 , COM A:554 , HOH A:600 , HOH A:4194 , 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:647 , ALA D:144 , VAL D:145 , VAL D:146 , GLN D:147 , GLN D:230 , MET D:233 , ALA D:243 , HOH D:571 , HOH D:647 , HOH D:670 , HOH D:713 , HOH D:721 , HOH D:723
BINDING SITE FOR RESIDUE F43 D 553
22
CC4
SOFTWARE
ARG A:225 , LYS A:256 , MHS A:257 , ARG D:270 , LEU D:320 , MET D:324 , PHE D:443 , MET D:480 , ASN D:481 , VAL D:482 , HOH D:570 , HOH D:575 , HOH D:583 , HOH D:632 , HOH D:664 , PHE E:362 , TYR E:367 , GLY E:368 , GLY E:369 , HIS E:379 , ILE E:380
BINDING SITE FOR RESIDUE TP7 D 554
23
CC5
SOFTWARE
F43 A:1 , HOH A:4189 , HOH A:4193 , TYR D:333 , PHE D:443 , TYR D:444 , HOH D:760 , PHE E:361 , SER E:365 , TYR E:367 , LEU F:117 , ARG F:120 , HOH F:4187 , HOH F:4188
BINDING SITE FOR RESIDUE COM D 555
24
CC6
SOFTWARE
ARG A:225 , LYS A:256 , MHS A:257 , ARG D:270 , MET D:324 , PHE D:330 , PHE D:443 , MET D:480 , ASN D:481 , VAL D:482 , HOH D:570 , HOH D:575 , HOH D:583 , HOH D:632 , HOH D:664 , PHE E:362 , GLY E:368 , GLY E:369 , HIS E:379 , ILE E:380
BINDING SITE FOR RESIDUE TXZ D 556
25
CC7
SOFTWARE
TYR D:348
BINDING SITE FOR RESIDUE EDO D 557
26
CC8
SOFTWARE
LYS D:22 , ARG F:147 , GLY F:166 , GLU F:207
BINDING SITE FOR RESIDUE EDO D 558
27
CC9
SOFTWARE
HOH E:2200 , HOH E:2328 , HOH E:3583 , HOH E:3584 , HOH E:3585
BINDING SITE FOR RESIDUE MG E 444
28
DC1
SOFTWARE
ASP E:271 , HOH E:1466 , HOH E:1684 , HOH E:3695 , HOH E:4090
BINDING SITE FOR RESIDUE MG E 445
29
DC2
SOFTWARE
GLU F:30 , HOH F:1294 , HOH F:3551 , HOH F:3552 , HOH F:3553 , HOH F:3554
BINDING SITE FOR RESIDUE MG F 250
30
DC3
SOFTWARE
LYS F:132 , HOH F:1243
BINDING SITE FOR RESIDUE EDO F 251
31
DC4
SOFTWARE
HOH F:832
BINDING SITE FOR RESIDUE EDO F 252
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
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_d3m2ua2 (A:270-549)
1b: SCOP_d3m2ud2 (D:270-549)
2a: SCOP_d3m2ub2 (B:189-443)
2b: SCOP_d3m2ue2 (E:189-443)
3a: SCOP_d3m2ua1 (A:2-269)
3b: SCOP_d3m2ud1 (D:2-269)
4a: SCOP_d3m2ub1 (B:2-188)
4b: SCOP_d3m2ue1 (E:2-188)
5a: SCOP_d3m2uc_ (C:)
5b: SCOP_d3m2uf_ (F:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
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
d3m2ua2
A:270-549
1b
d3m2ud2
D:270-549
Protein domain
:
Beta chain
(13)
Methanobacterium thermoautotrophicum [TaxId: 145262]
(11)
2a
d3m2ub2
B:189-443
2b
d3m2ue2
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
d3m2ua1
A:2-269
3b
d3m2ud1
D:2-269
Protein domain
:
Beta chain
(13)
Methanobacterium thermoautotrophicum [TaxId: 145262]
(11)
4a
d3m2ub1
B:2-188
4b
d3m2ue1
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
d3m2uc_
C:
5b
d3m2uf_
F:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(5, 10)
Info
all PFAM domains
1a: PFAM_MCR_alpha_3m2uD01 (D:316-441)
1b: PFAM_MCR_alpha_3m2uD02 (D:316-441)
2a: PFAM_MCR_alpha_N_3m2uD03 (D:2-268)
2b: PFAM_MCR_alpha_N_3m2uD04 (D:2-268)
3a: PFAM_MCR_beta_3m2uE01 (E:189-442)
3b: PFAM_MCR_beta_3m2uE02 (E:189-442)
4a: PFAM_MCR_beta_N_3m2uE03 (E:6-187)
4b: PFAM_MCR_beta_N_3m2uE04 (E:6-187)
5a: PFAM_MCR_gamma_3m2uF01 (F:2-247)
5b: PFAM_MCR_gamma_3m2uF02 (F:2-247)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: MCR_alpha]
(8)
Family
:
MCR_alpha
(8)
Methanothermobacter marburgensis (strain DSM 2133 / 14651 / NBRC 100331 / OCM 82 / Marburg) (Methano
(8)
1a
MCR_alpha-3m2uD01
D:316-441
1b
MCR_alpha-3m2uD02
D:316-441
Clan
:
no clan defined [family: MCR_alpha_N]
(8)
Family
:
MCR_alpha_N
(8)
Methanothermobacter marburgensis (strain DSM 2133 / 14651 / NBRC 100331 / OCM 82 / Marburg) (Methano
(8)
2a
MCR_alpha_N-3m2uD03
D:2-268
2b
MCR_alpha_N-3m2uD04
D:2-268
Clan
:
no clan defined [family: MCR_beta]
(8)
Family
:
MCR_beta
(8)
Methanothermobacter marburgensis (strain DSM 2133 / 14651 / NBRC 100331 / OCM 82 / Marburg) (Methano
(8)
3a
MCR_beta-3m2uE01
E:189-442
3b
MCR_beta-3m2uE02
E:189-442
Clan
:
no clan defined [family: MCR_beta_N]
(8)
Family
:
MCR_beta_N
(8)
Methanothermobacter marburgensis (strain DSM 2133 / 14651 / NBRC 100331 / OCM 82 / Marburg) (Methano
(8)
4a
MCR_beta_N-3m2uE03
E:6-187
4b
MCR_beta_N-3m2uE04
E:6-187
Clan
:
no clan defined [family: MCR_gamma]
(8)
Family
:
MCR_gamma
(8)
Methanothermobacter marburgensis (strain DSM 2133 / 14651 / NBRC 100331 / OCM 82 / Marburg) (Methano
(8)
5a
MCR_gamma-3m2uF01
F:2-247
5b
MCR_gamma-3m2uF02
F:2-247
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Chain E
Chain F
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (467 KB)
Header - Asym.Unit
Biol.Unit 1 (455 KB)
Header - Biol.Unit 1
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
3M2U
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help