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1XVF
Asym. Unit
Info
Asym.Unit (381 KB)
Biol.Unit 1 (374 KB)
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(1)
Title
:
SOLUBLE METHANE MONOOXYGENASE HYDROXYLASE: CHLOROPROPANOL 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
:
2.00
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, Cavities, Product, 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
(2, 12)
Info
All Hetero Components
1a: 3-CHLOROPROPANOL (3CLa)
1b: 3-CHLOROPROPANOL (3CLb)
1c: 3-CHLOROPROPANOL (3CLc)
1d: 3-CHLOROPROPANOL (3CLd)
1e: 3-CHLOROPROPANOL (3CLe)
1f: 3-CHLOROPROPANOL (3CLf)
1g: 3-CHLOROPROPANOL (3CLg)
1h: 3-CHLOROPROPANOL (3CLh)
2a: FE (III) ION (FEa)
2b: FE (III) ION (FEb)
2c: FE (III) ION (FEc)
2d: FE (III) ION (FEd)
View:
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Label:
No.
Name
Count
Type
Full Name
1
3CL
8
Ligand/Ion
3-CHLOROPROPANOL
2
FE
4
Ligand/Ion
FE (III) ION
[
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Sites
(12, 12)
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)
View:
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Label:
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 , 3CL A:1302 , 3CL A:2002 , HOH A:2004
BINDING SITE FOR RESIDUE FE A 1170
02
AC2
SOFTWARE
GLU A:114 , GLU A:144 , HIS A:147 , FE A:1170 , 3CL A:1302 , 3CL A:2002 , HOH A:2003 , HOH A:2004
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 , 3CL B:1303 , HOH B:1307
BINDING SITE FOR RESIDUE FE B 1174
04
AC4
SOFTWARE
GLU B:114 , GLU B:144 , HIS B:147 , FE B:1174 , 3CL B:1303 , HOH B:1306 , HOH B:1307
BINDING SITE FOR RESIDUE FE B 1175
05
AC5
SOFTWARE
VAL A:106 , LEU A:110 , VAL A:285 , LEU A:286
BINDING SITE FOR RESIDUE 3CL A 1300
06
AC6
SOFTWARE
LYS A:98 , GLU A:101 , THR A:102 , MET A:288 , LEU A:289 , TYR A:347 , LEU A:361 , HOH A:2038
BINDING SITE FOR RESIDUE 3CL A 1301
07
AC7
SOFTWARE
GLU A:114 , GLU A:144 , PHE A:192 , LEU A:204 , GLU A:209 , THR A:213 , FE A:1170 , FE A:1171 , HOH A:2004
BINDING SITE FOR RESIDUE 3CL A 1302
08
AC8
SOFTWARE
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:1306 , HOH B:1307 , HOH B:1537
BINDING SITE FOR RESIDUE 3CL B 1303
09
AC9
SOFTWARE
LYS B:98 , THR B:102 , LEU B:289 , GLY B:293 , LEU B:361 , HOH B:1309
BINDING SITE FOR RESIDUE 3CL B 1304
10
BC1
SOFTWARE
VAL B:106 , LEU B:110 , PHE B:282 , VAL B:285 , LEU B:286
BINDING SITE FOR RESIDUE 3CL B 1305
11
BC2
SOFTWARE
ASN B:24 , TRP D:117 , ARG D:118 , ASP D:121 , HOH D:1317 , HOH D:1439
BINDING SITE FOR RESIDUE 3CL D 1306
12
BC3
SOFTWARE
LEU A:110 , GLY A:113 , GLU A:114 , GLU A:144 , PHE A:188 , PHE A:192 , GLU A:209 , FE A:1170 , FE A:1171 , HOH A:2004
BINDING SITE FOR RESIDUE 3CL A 2002
[
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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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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_d1xvfa_ (A:)
1b: SCOP_d1xvfb_ (B:)
2a: SCOP_d1xvfc_ (C:)
2b: SCOP_d1xvfd_ (D:)
3a: SCOP_d1xvfe_ (E:)
3b: SCOP_d1xvff_ (F:)
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(
)
Protein Domains
(
)
(
)
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
d1xvfa_
A:
1b
d1xvfb_
B:
Protein domain
:
Methane monooxygenase hydrolase beta subunit
(29)
Methylococcus capsulatus [TaxId: 414]
(27)
2a
d1xvfc_
C:
2b
d1xvfd_
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
d1xvfe_
E:
3b
d1xvff_
F:
[
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CATH Domains
(3, 8)
Info
all CATH domains
1a: CATH_1xvfC00 (C:2-389)
1b: CATH_1xvfD00 (D:2-389)
1c: CATH_1xvfA00 (A:18-527)
1d: CATH_1xvfB00 (B:18-527)
2a: CATH_1xvfE01 (E:4-71)
2b: CATH_1xvfF01 (F:4-71)
3a: CATH_1xvfE02 (E:72-144)
3b: CATH_1xvfF02 (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
1xvfC00
C:2-389
1b
1xvfD00
D:2-389
1c
1xvfA00
A:18-527
1d
1xvfB00
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
1xvfE01
E:4-71
2b
1xvfF01
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
1xvfE02
E:72-144
3b
1xvfF02
F:72-144
[
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]
Pfam Domains
(2, 6)
Info
all PFAM domains
1a: PFAM_Phenol_Hydrox_1xvfB01 (B:36-263)
1b: PFAM_Phenol_Hydrox_1xvfB02 (B:36-263)
1c: PFAM_Phenol_Hydrox_1xvfD01 (D:71-308)
1d: PFAM_Phenol_Hydrox_1xvfD02 (D:71-308)
2a: PFAM_MeMO_Hyd_G_1xvfF01 (F:6-166)
2b: PFAM_MeMO_Hyd_G_1xvfF02 (F:6-166)
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Clans
(
)
(
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(
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(
)
Organisms
(
)
(
)
Clan
:
Ferritin
(185)
Family
:
Phenol_Hydrox
(21)
Methylococcus capsulatus
(11)
1a
Phenol_Hydrox-1xvfB01
B:36-263
1b
Phenol_Hydrox-1xvfB02
B:36-263
1c
Phenol_Hydrox-1xvfD01
D:71-308
1d
Phenol_Hydrox-1xvfD02
D:71-308
Clan
:
no clan defined [family: MeMO_Hyd_G]
(13)
Family
:
MeMO_Hyd_G
(13)
Methylococcus capsulatus
(11)
2a
MeMO_Hyd_G-1xvfF01
F:6-166
2b
MeMO_Hyd_G-1xvfF02
F:6-166
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