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2GC7
Biol. Unit 3
Info
Asym.Unit (509 KB)
Biol.Unit 1 (132 KB)
Biol.Unit 2 (132 KB)
Biol.Unit 3 (133 KB)
Biol.Unit 4 (133 KB)
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(1)
Title
:
SUBSTRATE REDUCED, COPPER FREE COMPLEX OF METHYLAMINE DEHYDROGENASE, AMICYANIN AND CYTOCHROME C551I FROM PARACOCCUS DENITRIFICANS.
Authors
:
Z. Chen, R. Durley, V. L. Davidson, F. S. Mathews
Date
:
13 Mar 06 (Deposition) - 06 Feb 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Biol. Unit 3: I,J,K,L (1x)
Biol. Unit 4: M,N,O,P (1x)
Keywords
:
Electron Transfer, Methylamine Dehydrogenase, Cytochrome, Amicyanin, Oxidoreductase, Electron Transport
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Z. Chen, R. Durley, V. L. Davidson, F. S. Mathews
Structral Comparison Of The Oxidized Ternary Electron Transfer Complex Of Methylamine Dehydrogenase, Amicyanin And Cytochrome C551I From Paracoccus Denitrificans With The Substrate-Reduced, Copper Free Complex At 1. 9 A Resolution.
To Be Published
(for further references see the
PDB file header
)
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Hetero Components
(2, 2)
Info
All Hetero Components
1a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
1b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
1c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
1d: PROTOPORPHYRIN IX CONTAINING FE (HEMd)
2a: SODIUM ION (NAa)
2b: SODIUM ION (NAb)
2c: SODIUM ION (NAc)
2d: SODIUM ION (NAd)
3a: 2-AMINO-3-(6,7-DIOXO-6,7-DIHYDRO-1... (TRQa)
3b: 2-AMINO-3-(6,7-DIOXO-6,7-DIHYDRO-1... (TRQb)
3c: 2-AMINO-3-(6,7-DIOXO-6,7-DIHYDRO-1... (TRQc)
3d: 2-AMINO-3-(6,7-DIOXO-6,7-DIHYDRO-1... (TRQd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
HEM
1
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
2
NA
-1
Ligand/Ion
SODIUM ION
3
TRQ
1
Mod. Amino Acid
2-AMINO-3-(6,7-DIOXO-6,7-DIHYDRO-1H-INDOL-3-YL)-PROPIONIC ACID
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Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC7 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLU K:31 , GLY L:72 , ASP L:75 , TYR L:77 , HOH L:1051 , HOH L:1475
BINDING SITE FOR RESIDUE NA L 601
2
AC7
SOFTWARE
MET L:56 , CYS L:57 , CYS L:60 , HIS L:61 , PRO L:71 , TRP L:78 , THR L:79 , TYR L:80 , ASN L:83 , LEU L:89 , ALA L:97 , THR L:98 , GLN L:100 , MET L:101 , HOH L:1475 , HOH L:2048
BINDING SITE FOR RESIDUE HEM L 200
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: CYTC (L:30-124)
2: COPPER_BLUE (K:85-98)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CYTC
PS51007
Cytochrome c family profile.
CYCL_PARDE
52-146
1
-
-
L:30-124
-
2
COPPER_BLUE
PS00196
Type-1 copper (blue) proteins signature.
AMCY_PARDE
111-124
1
-
-
K:85-98
-
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Exons
(0, 0)
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(4, 16)
Info
All SCOP Domains
1a: SCOP_d2gc7d_ (D:)
1b: SCOP_d2gc7h_ (H:)
1c: SCOP_d2gc7l_ (L:)
1d: SCOP_d2gc7p_ (P:)
2a: SCOP_d2gc7a_ (A:)
2b: SCOP_d2gc7e_ (E:)
2c: SCOP_d2gc7i_ (I:)
2d: SCOP_d2gc7m_ (M:)
3a: SCOP_d2gc7c_ (C:)
3b: SCOP_d2gc7g_ (G:)
3c: SCOP_d2gc7k_ (K:)
3d: SCOP_d2gc7o_ (O:)
4a: SCOP_d2gc7b_ (B:)
4b: SCOP_d2gc7f_ (F:)
4c: SCOP_d2gc7j_ (J:)
4d: SCOP_d2gc7n_ (N:)
View:
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Classes
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)
(
)
Folds
(
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(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Cytochrome c
(308)
Superfamily
:
Cytochrome c
(308)
Family
:
monodomain cytochrome c
(197)
Protein domain
:
Cytochrome c551
(13)
Paracoccus denitrificans [TaxId: 266]
(5)
1a
d2gc7d_
D:
1b
d2gc7h_
H:
1c
d2gc7l_
L:
1d
d2gc7p_
P:
Class
:
All beta proteins
(24004)
Fold
:
7-bladed beta-propeller
(245)
Superfamily
:
YVTN repeat-like/Quinoprotein amine dehydrogenase
(31)
Family
:
automated matches
(18)
Protein domain
:
automated matches
(18)
Paracoccus denitrificans [TaxId: 318586]
(18)
2a
d2gc7a_
A:
2b
d2gc7e_
E:
2c
d2gc7i_
I:
2d
d2gc7m_
M:
Fold
:
Cupredoxin-like
(545)
Superfamily
:
Cupredoxins
(543)
Family
:
Plastocyanin/azurin-like
(241)
Protein domain
:
Amicyanin
(34)
Paracoccus denitrificans [TaxId: 266]
(33)
3a
d2gc7c_
C:
3b
d2gc7g_
G:
3c
d2gc7k_
K:
3d
d2gc7o_
O:
Class
:
Small proteins
(3458)
Fold
:
Methylamine dehydrogenase, L chain
(68)
Superfamily
:
Methylamine dehydrogenase, L chain
(68)
Family
:
Methylamine dehydrogenase, L chain
(41)
Protein domain
:
automated matches
(32)
Paracoccus denitrificans [TaxId: 266]
(12)
4a
d2gc7b_
B:
4b
d2gc7f_
F:
4c
d2gc7j_
J:
4d
d2gc7n_
N:
[
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CATH Domains
(4, 16)
Info
all CATH domains
1a: CATH_2gc7D00 (D:1-147)
1b: CATH_2gc7H00 (H:1-147)
1c: CATH_2gc7L00 (L:1-147)
1d: CATH_2gc7P00 (P:1-147)
2a: CATH_2gc7A00 (A:5-386)
2b: CATH_2gc7E00 (E:5-386)
2c: CATH_2gc7I00 (I:5-386)
2d: CATH_2gc7M00 (M:5-386)
3a: CATH_2gc7B00 (B:7-131)
3b: CATH_2gc7F00 (F:7-131)
3c: CATH_2gc7J00 (J:7-131)
3d: CATH_2gc7N00 (N:7-131)
4a: CATH_2gc7C00 (C:1-105)
4b: CATH_2gc7G00 (G:1-105)
4c: CATH_2gc7K00 (K:1-105)
4d: CATH_2gc7O00 (O:1-105)
View:
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)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Cytochrome Bc1 Complex; Chain D, domain 2
(279)
Homologous Superfamily
:
Cytochrome c
(279)
Paracoccus denitrificans. Organism_taxid: 266. Paracoccus denitrificans. Organism_taxid: 266. Paracoccus denitrificans. Organism_taxid: 266.
(3)
1a
2gc7D00
D:1-147
1b
2gc7H00
H:1-147
1c
2gc7L00
L:1-147
1d
2gc7P00
P:1-147
Class
:
Mainly Beta
(13760)
Architecture
:
7 Propellor
(136)
Topology
:
Methylamine Dehydrogenase; Chain H
(136)
Homologous Superfamily
:
YVTN repeat-like/Quinoprotein amine dehydrogenase
(76)
Paracoccus denitrificans. Organism_taxid: 266. Paracoccus denitrificans. Organism_taxid: 266. Paracoccus denitrificans. Organism_taxid: 266.
(3)
2a
2gc7A00
A:5-386
2b
2gc7E00
E:5-386
2c
2gc7I00
I:5-386
2d
2gc7M00
M:5-386
Architecture
:
Sandwich
(5577)
Topology
:
Electron Transport Ethylamine Dehydrogenase
(43)
Homologous Superfamily
:
Electron Transport Ethylamine Dehydrogenase
(43)
Paracoccus denitrificans. Organism_taxid: 266. Paracoccus denitrificans. Organism_taxid: 266. Paracoccus denitrificans. Organism_taxid: 266.
(3)
3a
2gc7B00
B:7-131
3b
2gc7F00
F:7-131
3c
2gc7J00
J:7-131
3d
2gc7N00
N:7-131
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Cupredoxins - blue copper proteins
(420)
Paracoccus denitrificans. Organism_taxid: 266. Paracoccus denitrificans. Organism_taxid: 266. Paracoccus denitrificans. Organism_taxid: 266.
(3)
4a
2gc7C00
C:1-105
4b
2gc7G00
G:1-105
4c
2gc7K00
K:1-105
4d
2gc7O00
O:1-105
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Pfam Domains
(0, 0)
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all PFAM domains
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