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1XVE
Asym. Unit
Info
Asym.Unit (366 KB)
Biol.Unit 1 (359 KB)
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(1)
Title
:
SOLUBLE METHANE MONOOXYGENASE HYDROXYLASE: 3-BROMO-3-BUTENOL SOAKED STRUCTURE
Authors
:
M. H. Sazinsky, S. J. Lippard
Date
:
27 Oct 04 (Deposition) - 03 May 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Methane, Diiron, Four-Helix Bundle, Product Binding, Cavities, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. H. Sazinsky, S. J. Lippard
Product Bound Structures Of The Soluble Methane Monooxygenase Hydroxylase From Methylococcus Capsulatus (Bath): Protein Motion In The Alpha-Subunit
J. Am. Chem. Soc. V. 127 5814 2005
(for further references see the
PDB file header
)
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Hetero Components
(3, 16)
Info
All Hetero Components
1a: 3-BROMOBUT-3-EN-1-OL (3BBa)
1b: 3-BROMOBUT-3-EN-1-OL (3BBb)
1c: 3-BROMOBUT-3-EN-1-OL (3BBc)
1d: 3-BROMOBUT-3-EN-1-OL (3BBd)
1e: 3-BROMOBUT-3-EN-1-OL (3BBe)
1f: 3-BROMOBUT-3-EN-1-OL (3BBf)
1g: 3-BROMOBUT-3-EN-1-OL (3BBg)
1h: 3-BROMOBUT-3-EN-1-OL (3BBh)
1i: 3-BROMOBUT-3-EN-1-OL (3BBi)
1j: 3-BROMOBUT-3-EN-1-OL (3BBj)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
3a: FE (III) ION (FEa)
3b: FE (III) ION (FEb)
3c: FE (III) ION (FEc)
3d: FE (III) ION (FEd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
3BB
10
Ligand/Ion
3-BROMOBUT-3-EN-1-OL
2
CA
2
Ligand/Ion
CALCIUM ION
3
FE
4
Ligand/Ion
FE (III) ION
[
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Sites
(16, 16)
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)
View:
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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLN A:140 , GLU A:144 , GLU A:209 , GLU A:243 , HIS A:246 , FE A:1171 , 3BB A:1172 , HOH A:1177
BINDING SITE FOR RESIDUE FE A 1170
02
AC2
SOFTWARE
GLU A:114 , GLU A:144 , HIS A:147 , FE A:1170 , 3BB A:1172 , HOH A:1176 , HOH A:1177
BINDING SITE FOR RESIDUE FE A 1171
03
AC3
SOFTWARE
GLU B:144 , GLU B:209 , GLU B:243 , HIS B:246 , FE B:1175 , 3BB B:1176 , HOH B:1180
BINDING SITE FOR RESIDUE FE B 1174
04
AC4
SOFTWARE
GLU B:114 , GLU B:144 , HIS B:147 , FE B:1174 , 3BB B:1176 , HOH B:1179 , HOH B:1180
BINDING SITE FOR RESIDUE FE B 1175
05
AC5
SOFTWARE
ASN A:527 , ASN B:412 , SER B:428
BINDING SITE FOR RESIDUE CA A 673
06
AC6
SOFTWARE
GLU C:222 , HOH C:722
BINDING SITE FOR RESIDUE CA C 674
07
AC7
SOFTWARE
LEU A:110 , GLY A:113 , GLU A:114 , GLU A:144 , PHE A:188 , PHE A:192 , GLU A:209 , THR A:213 , FE A:1170 , FE A:1171 , HOH A:1177
BINDING SITE FOR RESIDUE 3BB A 1172
08
AC8
SOFTWARE
LEU B:110 , GLY B:113 , GLU B:114 , GLU B:144 , PHE B:188 , PHE B:192 , GLU B:209 , THR B:213 , FE B:1174 , FE B:1175 , HOH B:1179 , HOH B:1180 , HOH B:1232
BINDING SITE FOR RESIDUE 3BB B 1176
09
AC9
SOFTWARE
VAL B:106 , PHE B:109 , MET B:184 , LEU B:216 , VAL B:220 , PHE B:282 , LEU B:286 , LEU B:289
BINDING SITE FOR RESIDUE 3BB B 1177
10
BC1
SOFTWARE
LYS B:98 , GLU B:101 , THR B:102 , LEU B:289 , PHE B:359 , LEU B:361 , HOH B:1242
BINDING SITE FOR RESIDUE 3BB B 1178
11
BC2
SOFTWARE
PHE A:109 , LEU A:110 , LEU A:216 , PHE A:282 , LEU A:289
BINDING SITE FOR RESIDUE 3BB A 1173
12
BC3
SOFTWARE
LEU A:405 , PHE A:408 , ILE A:409 , PRO A:414 , ILE A:415 , PRO A:522
BINDING SITE FOR RESIDUE 3BB A 1174
13
BC4
SOFTWARE
LYS A:98 , GLU A:101 , THR A:102 , MET A:288 , LEU A:289 , PHE A:359 , ARG A:360 , LEU A:361 , HOH A:1244
BINDING SITE FOR RESIDUE 3BB A 1175
14
BC5
SOFTWARE
ARG C:122 , GLN C:125 , GLY C:126 , THR D:286 , ILE D:290 , GLN D:293
BINDING SITE FOR RESIDUE 3BB C 508
15
BC6
SOFTWARE
LEU C:102 , GLN C:293 , GLN D:125
BINDING SITE FOR RESIDUE 3BB D 509
16
BC7
SOFTWARE
VAL C:39 , THR C:40 , TYR C:55
BINDING SITE FOR RESIDUE 3BB C 510
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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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End label:
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
(3, 6)
Info
All SCOP Domains
1a: SCOP_d1xvea_ (A:)
1b: SCOP_d1xveb_ (B:)
2a: SCOP_d1xvec_ (C:)
2b: SCOP_d1xved_ (D:)
3a: SCOP_d1xvee_ (E:)
3b: SCOP_d1xvef_ (F:)
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Protein Domains
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Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Ferritin-like
(533)
Superfamily
:
Ferritin-like
(489)
Family
:
Ribonucleotide reductase-like
(185)
Protein domain
:
Methane monooxygenase hydrolase alpha subunit
(28)
Methylococcus capsulatus [TaxId: 414]
(26)
1a
d1xvea_
A:
1b
d1xveb_
B:
Protein domain
:
Methane monooxygenase hydrolase beta subunit
(29)
Methylococcus capsulatus [TaxId: 414]
(27)
2a
d1xvec_
C:
2b
d1xved_
D:
Fold
:
Open three-helical up-and-down bundle
(49)
Superfamily
:
Methane monooxygenase hydrolase, gamma subunit
(29)
Family
:
Methane monooxygenase hydrolase, gamma subunit
(29)
Protein domain
:
Methane monooxygenase hydrolase, gamma subunit
(29)
Methylococcus capsulatus [TaxId: 414]
(27)
3a
d1xvee_
E:
3b
d1xvef_
F:
[
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CATH Domains
(3, 8)
Info
all CATH domains
1a: CATH_1xveC00 (C:2-389)
1b: CATH_1xveD00 (D:2-389)
1c: CATH_1xveA00 (A:18-527)
1d: CATH_1xveB00 (B:18-527)
2a: CATH_1xveE01 (E:4-71)
2b: CATH_1xveF01 (F:4-71)
3a: CATH_1xveE02 (E:72-144)
3b: CATH_1xveF02 (F:72-144)
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)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Ribonucleotide Reductase, subunit A
(86)
Homologous Superfamily
:
Ribonucleotide Reductase, subunit A
(86)
Methylococcus capsulatus. Organism_taxid: 414. Methylococcus capsulatus. Organism_taxid: 414.
(22)
1a
1xveC00
C:2-389
1b
1xveD00
D:2-389
1c
1xveA00
A:18-527
1d
1xveB00
B:18-527
Architecture
:
Up-down Bundle
(3216)
Topology
:
Monooxygenase
(39)
Homologous Superfamily
:
[code=1.20.1280.10, no name defined]
(28)
Methylococcus capsulatus. Organism_taxid: 414. Methylococcus capsulatus. Organism_taxid: 414.
(22)
2a
1xveE01
E:4-71
2b
1xveF01
F:4-71
Homologous Superfamily
:
[code=1.20.1280.30, no name defined]
(28)
Methylococcus capsulatus. Organism_taxid: 414. Methylococcus capsulatus. Organism_taxid: 414.
(22)
3a
1xveE02
E:72-144
3b
1xveF02
F:72-144
[
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Pfam Domains
(2, 6)
Info
all PFAM domains
1a: PFAM_Phenol_Hydrox_1xveB01 (B:36-263)
1b: PFAM_Phenol_Hydrox_1xveB02 (B:36-263)
1c: PFAM_Phenol_Hydrox_1xveD01 (D:71-308)
1d: PFAM_Phenol_Hydrox_1xveD02 (D:71-308)
2a: PFAM_MeMO_Hyd_G_1xveF01 (F:6-166)
2b: PFAM_MeMO_Hyd_G_1xveF02 (F:6-166)
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Clans
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(
)
(
)
Clan
:
Ferritin
(185)
Family
:
Phenol_Hydrox
(21)
Methylococcus capsulatus
(11)
1a
Phenol_Hydrox-1xveB01
B:36-263
1b
Phenol_Hydrox-1xveB02
B:36-263
1c
Phenol_Hydrox-1xveD01
D:71-308
1d
Phenol_Hydrox-1xveD02
D:71-308
Clan
:
no clan defined [family: MeMO_Hyd_G]
(13)
Family
:
MeMO_Hyd_G
(13)
Methylococcus capsulatus
(11)
2a
MeMO_Hyd_G-1xveF01
F:6-166
2b
MeMO_Hyd_G-1xveF02
F:6-166
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