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Getting 'Biological Unit' information from database.
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Getting 'Hetero Component' information from database.
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3AYY
Asym. Unit
Info
Asym.Unit (638 KB)
Biol.Unit 1 (630 KB)
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(1)
Title
:
MEMBRANE-BOUND RESPIRATORY [NIFE] HYDROGENASE FROM HYDROGENOVIBRIO MARINUS IN A FERRICYANIDE-OXIDIZED CONDITION
Authors
:
Y. Shomura, K. S. Yoon, H. Nishihara, Y. Higuchi
Date
:
20 May 11 (Deposition) - 12 Oct 11 (Release) - 23 Nov 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.32
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Oxidoreductase, Membrane-Bound Ni-Fe Hydrogenase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Shomura, K. S. Yoon, H. Nishihara, Y. Higuchi
Structural Basis For A [4Fe-3S] Cluster In The Oxygen-Tolerant Membrane-Bound [Nife]-Hydrogenase
Nature V. 479 253 2011
[
close entry info
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Hetero Components
(10, 32)
Info
All Hetero Components
01a: NICKEL (III) ION (3NIa)
01b: NICKEL (III) ION (3NIb)
02a: CARBON MONOXIDE (CMOa)
02b: CARBON MONOXIDE (CMOb)
03a: CYANIDE ION (CYNa)
03b: CYANIDE ION (CYNb)
03c: CYANIDE ION (CYNc)
03d: CYANIDE ION (CYNd)
04a: FE3-S4 CLUSTER (F3Sa)
04b: FE3-S4 CLUSTER (F3Sb)
05a: FE (II) ION (FE2a)
05b: FE (II) ION (FE2b)
06a: GLYCEROL (GOLa)
06b: GLYCEROL (GOLb)
06c: GLYCEROL (GOLc)
06d: GLYCEROL (GOLd)
07a: MAGNESIUM ION (MGa)
07b: MAGNESIUM ION (MGb)
08a: OXYGEN ATOM (Oa)
08b: OXYGEN ATOM (Ob)
08c: OXYGEN ATOM (Oc)
08d: OXYGEN ATOM (Od)
08e: OXYGEN ATOM (Oe)
08f: OXYGEN ATOM (Of)
08g: OXYGEN ATOM (Og)
08h: OXYGEN ATOM (Oh)
08i: OXYGEN ATOM (Oi)
08j: OXYGEN ATOM (Oj)
09a: FE4-S3 CLUSTER (SF3a)
09b: FE4-S3 CLUSTER (SF3b)
10a: IRON/SULFUR CLUSTER (SF4a)
10b: IRON/SULFUR CLUSTER (SF4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
3NI
2
Ligand/Ion
NICKEL (III) ION
2
CMO
2
Ligand/Ion
CARBON MONOXIDE
3
CYN
4
Ligand/Ion
CYANIDE ION
4
F3S
2
Ligand/Ion
FE3-S4 CLUSTER
5
FE2
2
Ligand/Ion
FE (II) ION
6
GOL
4
Ligand/Ion
GLYCEROL
7
MG
2
Ligand/Ion
MAGNESIUM ION
8
O
10
Ligand/Ion
OXYGEN ATOM
9
SF3
2
Ligand/Ion
FE4-S3 CLUSTER
10
SF4
2
Ligand/Ion
IRON/SULFUR CLUSTER
[
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
CYS A:79 , CYS A:593 , 3NI A:602 , CMO A:603 , CYN A:604 , CYN A:605 , O A:606 , O A:609
BINDING SITE FOR RESIDUE FE2 A 601
02
AC2
SOFTWARE
CYS A:76 , CYS A:79 , CYS A:590 , CYS A:593 , FE2 A:601 , O A:606 , O A:607 , O A:608 , O A:609 , O A:610
BINDING SITE FOR RESIDUE 3NI A 602
03
AC3
SOFTWARE
CYS A:79 , CYS A:82 , HIS A:83 , LEU A:526 , VAL A:544 , PRO A:545 , CYS A:593 , FE2 A:601 , CYN A:604 , CYN A:605
BINDING SITE FOR RESIDUE CMO A 603
04
AC4
SOFTWARE
CYS A:79 , ALA A:521 , PRO A:522 , ARG A:523 , FE2 A:601 , CMO A:603 , CYN A:605 , O A:606
BINDING SITE FOR RESIDUE CYN A 604
05
AC5
SOFTWARE
ARG A:523 , VAL A:544 , PRO A:545 , THR A:546 , CYS A:593 , FE2 A:601 , CMO A:603 , CYN A:604 , O A:606
BINDING SITE FOR RESIDUE CYN A 605
06
AC6
SOFTWARE
CYS A:79 , ARG A:523 , CYS A:590 , CYS A:593 , FE2 A:601 , 3NI A:602 , CYN A:604 , CYN A:605 , O A:607 , O A:609 , O A:610
BINDING SITE FOR RESIDUE O A 606
07
AC7
SOFTWARE
CYS A:76 , CYS A:590 , ALA A:592 , CYS A:593 , 3NI A:602 , O A:606 , O A:608 , O A:609 , O A:610
BINDING SITE FOR RESIDUE O A 607
08
AC8
SOFTWARE
GLU A:28 , CYS A:76 , CYS A:590 , LEU A:591 , ALA A:592 , CYS A:593 , 3NI A:602 , O A:607 , O A:610
BINDING SITE FOR RESIDUE O A 608
09
AC9
SOFTWARE
CYS A:76 , CYS A:79 , CYS A:590 , CYS A:593 , FE2 A:601 , 3NI A:602 , O A:606 , O A:607 , O A:610
BINDING SITE FOR RESIDUE O A 609
10
BC1
SOFTWARE
CYS A:76 , CYS A:79 , CYS A:590 , CYS A:593 , 3NI A:602 , O A:606 , O A:607 , O A:608 , O A:609
BINDING SITE FOR RESIDUE O A 610
11
BC2
SOFTWARE
LYS A:310 , GLN A:319 , ASP A:482 , HOH A:851 , HOH A:1630
BINDING SITE FOR RESIDUE GOL A 702
12
BC3
SOFTWARE
ILE A:242 , ASN A:243 , ILE A:244 , ASP A:245 , GLY A:246 , SER A:496 , HOH A:1055 , HOH A:1139 , ARG B:220
BINDING SITE FOR RESIDUE GOL A 703
13
BC4
SOFTWARE
GLU A:57 , CYS A:542 , HIS A:596 , HOH A:746 , HOH A:764 , HOH A:795
BINDING SITE FOR RESIDUE MG A 701
14
BC5
SOFTWARE
CYS B:23 , THR B:24 , CYS B:25 , CYS B:26 , GLU B:82 , SER B:120 , CYS B:121 , CYS B:126 , GLY B:157 , CYS B:158
BINDING SITE FOR RESIDUE SF3 B 301
15
BC6
SOFTWARE
LYS A:227 , THR B:235 , ASN B:237 , CYS B:239 , TRP B:244 , PRO B:251 , CYS B:258 , ILE B:259 , CYS B:261
BINDING SITE FOR RESIDUE F3S B 308
16
BC7
SOFTWARE
HIS B:196 , CYS B:199 , ARG B:202 , CYS B:224 , LEU B:225 , CYS B:230
BINDING SITE FOR RESIDUE SF4 B 309
17
BC8
SOFTWARE
GLU C:57 , CYS C:542 , HIS C:596 , HOH C:699 , HOH C:757 , HOH C:758
BINDING SITE FOR RESIDUE MG C 701
18
BC9
SOFTWARE
CYS C:79 , CYS C:593 , 3NI C:602 , CMO C:603 , CYN C:604 , CYN C:605 , O C:606 , O C:609
BINDING SITE FOR RESIDUE FE2 C 601
19
CC1
SOFTWARE
CYS C:76 , CYS C:79 , CYS C:590 , CYS C:593 , FE2 C:601 , O C:606 , O C:607 , O C:608 , O C:609 , O C:610
BINDING SITE FOR RESIDUE 3NI C 602
20
CC2
SOFTWARE
CYS C:79 , CYS C:82 , HIS C:83 , LEU C:526 , VAL C:544 , PRO C:545 , CYS C:593 , FE2 C:601 , CYN C:604 , CYN C:605
BINDING SITE FOR RESIDUE CMO C 603
21
CC3
SOFTWARE
CYS C:79 , ALA C:521 , PRO C:522 , ARG C:523 , FE2 C:601 , CMO C:603 , CYN C:605 , O C:606
BINDING SITE FOR RESIDUE CYN C 604
22
CC4
SOFTWARE
VAL C:544 , PRO C:545 , THR C:546 , CYS C:593 , FE2 C:601 , CMO C:603 , CYN C:604 , O C:606
BINDING SITE FOR RESIDUE CYN C 605
23
CC5
SOFTWARE
CYS C:79 , ARG C:523 , CYS C:590 , CYS C:593 , FE2 C:601 , 3NI C:602 , CYN C:604 , CYN C:605 , O C:607 , O C:609 , O C:610
BINDING SITE FOR RESIDUE O C 606
24
CC6
SOFTWARE
CYS C:76 , CYS C:590 , ALA C:592 , CYS C:593 , 3NI C:602 , O C:606 , O C:608 , O C:609 , O C:610
BINDING SITE FOR RESIDUE O C 607
25
CC7
SOFTWARE
GLU C:28 , CYS C:76 , CYS C:590 , LEU C:591 , ALA C:592 , CYS C:593 , 3NI C:602 , O C:607 , O C:610
BINDING SITE FOR RESIDUE O C 608
26
CC8
SOFTWARE
CYS C:76 , CYS C:79 , CYS C:590 , CYS C:593 , FE2 C:601 , 3NI C:602 , O C:606 , O C:607 , O C:610
BINDING SITE FOR RESIDUE O C 609
27
CC9
SOFTWARE
CYS C:76 , CYS C:79 , CYS C:590 , CYS C:593 , 3NI C:602 , O C:606 , O C:607 , O C:608 , O C:609
BINDING SITE FOR RESIDUE O C 610
28
DC1
SOFTWARE
LYS C:310 , GLN C:319 , TYR C:475 , ASP C:482 , HOH C:789
BINDING SITE FOR RESIDUE GOL C 702
29
DC2
SOFTWARE
ILE C:242 , ASN C:243 , ILE C:244 , ASP C:245 , SER C:496 , HOH C:1514 , ARG D:220
BINDING SITE FOR RESIDUE GOL C 703
30
DC3
SOFTWARE
CYS D:23 , THR D:24 , CYS D:25 , CYS D:26 , GLU D:82 , SER D:120 , CYS D:121 , CYS D:126 , GLY D:157 , CYS D:158
BINDING SITE FOR RESIDUE SF3 D 301
31
DC4
SOFTWARE
LYS C:227 , THR D:235 , ASN D:237 , CYS D:239 , TRP D:244 , PRO D:251 , CYS D:258 , ILE D:259 , CYS D:261
BINDING SITE FOR RESIDUE F3S D 308
32
DC5
SOFTWARE
HIS D:196 , CYS D:199 , ARG D:202 , CYS D:224 , LEU D:225 , CYS D:230
BINDING SITE FOR RESIDUE SF4 D 309
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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End label:
Sorry, no Info available
[
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Exons
(0, 0)
Info
All Exons
View:
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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
(2, 4)
Info
All SCOP Domains
1a: SCOP_d3ayyb_ (B:)
1b: SCOP_d3ayyd_ (D:)
2a: SCOP_d3ayya_ (A:)
2b: SCOP_d3ayyc_ (C:)
View:
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Classes
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
HydA/Nqo6-like
(51)
Superfamily
:
HydA/Nqo6-like
(51)
Family
:
automated matches
(8)
Protein domain
:
automated matches
(8)
Hydrogenovibrio marinus [TaxId: 28885]
(3)
1a
d3ayyb_
B:
1b
d3ayyd_
D:
Fold
:
HydB/Nqo4-like
(55)
Superfamily
:
HydB/Nqo4-like
(55)
Family
:
automated matches
(11)
Protein domain
:
automated matches
(11)
Hydrogenovibrio marinus [TaxId: 28885]
(3)
2a
d3ayya_
A:
2b
d3ayyc_
C:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Label:
Sorry, no Info available
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Atom Selection
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select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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