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3HRD
Asym. Unit
Info
Asym.Unit (398 KB)
Biol.Unit 1 (389 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF NICOTINATE DEHYDROGENASE
Authors
:
N. Wagener, A. J. Pierik, R. Hille, H. Dobbek
Date
:
09 Jun 09 (Deposition) - 30 Jun 09 (Release) - 21 Jul 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D,E,F,G,H (1x)
Keywords
:
Selenium Ligand, 2Fe-2S, Iron, Iron-Sulfur, Metal-Binding, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. Wagener, A. J. Pierik, A. Ibdah, R. Hille, H. Dobbek
The Mo-Se Active Site Of Nicotinate Dehydrogenase
Proc. Natl. Acad. Sci. Usa V. 106 11055 2009
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(9, 20)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
2a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
2b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
3a: FE2/S2 (INORGANIC) CLUSTER (FESa)
3b: FE2/S2 (INORGANIC) CLUSTER (FESb)
3c: FE2/S2 (INORGANIC) CLUSTER (FESc)
3d: FE2/S2 (INORGANIC) CLUSTER (FESd)
4a: PTERIN CYTOSINE DINUCLEOTIDE (MCNa)
4b: PTERIN CYTOSINE DINUCLEOTIDE (MCNb)
5a: MAGNESIUM ION (MGa)
5b: MAGNESIUM ION (MGb)
6a: DIOXOTHIOMOLYBDENUM(VI) ION (MOSa)
6b: DIOXOTHIOMOLYBDENUM(VI) ION (MOSb)
7a: NICOTINIC ACID (NIOa)
7b: NICOTINIC ACID (NIOb)
8a: NITRATE ION (NO3a)
8b: NITRATE ION (NO3b)
8c: NITRATE ION (NO3c)
9a: SELENIUM ATOM (SEa)
9b: SELENIUM ATOM (SEb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
1
Ligand/Ion
CALCIUM ION
2
FAD
2
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
3
FES
4
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
4
MCN
2
Ligand/Ion
PTERIN CYTOSINE DINUCLEOTIDE
5
MG
2
Ligand/Ion
MAGNESIUM ION
6
MOS
2
Ligand/Ion
DIOXOTHIOMOLYBDENUM(VI) ION
7
NIO
2
Ligand/Ion
NICOTINIC ACID
8
NO3
3
Ligand/Ion
NITRATE ION
9
SE
2
Ligand/Ion
SELENIUM ATOM
[
close Hetero Component info
]
Sites
(20, 20)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PHE A:239 , GLY A:240 , ALA A:349 , PHE A:350 , ARG A:351 , GLU B:289 , MOS B:920 , MCN B:921
BINDING SITE FOR RESIDUE SE A 922
02
AC2
SOFTWARE
ARG A:278 , HIS A:279 , VAL A:316 , GLY A:348 , ALA A:349 , PHE A:350 , PHE A:353 , GLY A:354 , GLN A:357
BINDING SITE FOR RESIDUE NO3 A 5658
03
AC3
SOFTWARE
THR A:207 , ASN A:209 , ASP A:213 , LYS A:242 , LEU A:243 , ASP A:244 , GLN A:248 , HOH A:448
BINDING SITE FOR RESIDUE MG A 426
04
AC4
SOFTWARE
THR A:306 , TYR A:309 , ALA A:310 , SER A:347
BINDING SITE FOR RESIDUE MG A 427
05
AC5
SOFTWARE
GLN A:208 , GLY A:240 , LEU A:243 , PHE A:353 , SE A:922 , THR B:84 , SER B:85 , ALA B:86 , GLU B:289 , MCN B:921
BINDING SITE FOR RESIDUE MOS B 920
06
AC6
SOFTWARE
GLY A:237 , GLY A:238 , PHE A:239 , ARG A:351 , SE A:922 , ILE B:45 , GLY B:46 , GLN B:47 , GLY B:48 , SER B:49 , THR B:84 , SER B:85 , ALA B:86 , SER B:87 , ARG B:88 , GLN B:89 , THR B:90 , VAL B:211 , THR B:213 , ILE B:215 , ASN B:216 , MET B:219 , VAL B:220 , GLN B:223 , ALA B:284 , LYS B:285 , GLY B:286 , VAL B:287 , GLY B:288 , GLU B:289 , HOH B:384 , HOH B:446 , MOS B:920 , GLN D:100 , CYS D:138
BINDING SITE FOR RESIDUE MCN B 921
07
AC7
SOFTWARE
TYR A:312 , ALA A:315 , ARG A:319 , PHE A:353 , HOH A:513 , ASN B:17 , THR B:18 , LEU B:20
BINDING SITE FOR RESIDUE NIO B 5661
08
AC8
SOFTWARE
ILE C:29 , ALA C:31 , GLY C:32 , GLY C:33 , THR C:34 , ASP C:35 , LEU C:36 , ILE C:38 , ALA C:73 , PHE C:77 , VAL C:100 , GLY C:101 , ILE C:105 , THR C:110 , GLY C:113 , ASN C:114 , SER C:116 , THR C:117 , GLY C:122 , ASP C:123 , ARG C:160 , ILE C:168 , MET C:169 , LYS C:187 , ALA C:195 , HOH C:303 , HOH C:329 , HOH C:359 , HOH C:361 , HOH C:388 , GLU D:44 , GLY D:45 , GLU D:46
BINDING SITE FOR RESIDUE FAD C 900
09
AC9
SOFTWARE
CYS C:222 , ARG C:265 , PRO C:266 , SER C:267 , VAL C:268 , LYS C:271
BINDING SITE FOR RESIDUE NO3 C 5659
10
BC1
SOFTWARE
ILE A:186 , GLN D:100 , CYS D:101 , GLY D:102 , CYS D:104 , CYS D:136 , ARG D:137 , CYS D:138
BINDING SITE FOR RESIDUE FES D 907
11
BC2
SOFTWARE
GLY D:41 , CYS D:42 , SER D:43 , GLY D:45 , GLU D:46 , CYS D:47 , GLY D:48 , CYS D:50 , THR D:60 , CYS D:62
BINDING SITE FOR RESIDUE FES D 908
12
BC3
SOFTWARE
PHE E:239 , GLY E:240 , ALA E:349 , PHE E:350 , ARG E:351 , GLU F:289 , MOS F:920 , MCN F:921
BINDING SITE FOR RESIDUE SE E 922
13
BC4
SOFTWARE
GLU A:198 , VAL E:15 , GLU E:19 , HOH E:441 , HOH E:757 , VAL F:70 , THR F:71 , TRP F:72
BINDING SITE FOR RESIDUE NIO E 5660
14
BC5
SOFTWARE
ARG E:278 , HIS E:279 , VAL E:316 , GLY E:348 , ALA E:349 , PHE E:350 , GLY E:354 , GLN E:357
BINDING SITE FOR RESIDUE NO3 E 5662
15
BC6
SOFTWARE
THR E:207 , ASN E:209 , ASP E:213 , LYS E:242 , LEU E:243 , ASP E:244 , GLN E:248
BINDING SITE FOR RESIDUE CA E 5663
16
BC7
SOFTWARE
GLN E:208 , GLY E:240 , LEU E:243 , SE E:922 , THR F:84 , SER F:85 , ALA F:86 , GLU F:289 , MCN F:921
BINDING SITE FOR RESIDUE MOS F 920
17
BC8
SOFTWARE
GLY E:238 , PHE E:239 , ARG E:351 , SE E:922 , ILE F:45 , GLY F:46 , GLN F:47 , GLY F:48 , SER F:49 , THR F:84 , SER F:85 , ALA F:86 , SER F:87 , ARG F:88 , GLN F:89 , THR F:90 , VAL F:211 , THR F:213 , ILE F:215 , ASN F:216 , MET F:219 , VAL F:220 , GLN F:223 , ALA F:284 , LYS F:285 , GLY F:286 , VAL F:287 , GLY F:288 , GLU F:289 , HOH F:333 , HOH F:895 , MOS F:920 , GLN H:100 , CYS H:138
BINDING SITE FOR RESIDUE MCN F 921
18
BC9
SOFTWARE
ILE G:29 , ALA G:31 , GLY G:32 , GLY G:33 , THR G:34 , ASP G:35 , LEU G:36 , ILE G:38 , ILE G:53 , PHE G:77 , VAL G:100 , GLY G:101 , ILE G:105 , THR G:110 , GLY G:113 , ASN G:114 , SER G:116 , THR G:117 , GLY G:122 , ASP G:123 , ARG G:160 , ILE G:168 , MET G:169 , LYS G:187 , ALA G:195 , HOH G:297 , GLU H:44 , GLY H:45 , GLU H:46
BINDING SITE FOR RESIDUE FAD G 900
19
CC1
SOFTWARE
ILE E:186 , GLN H:100 , CYS H:101 , GLY H:102 , CYS H:104 , CYS H:136 , ARG H:137 , CYS H:138
BINDING SITE FOR RESIDUE FES H 907
20
CC2
SOFTWARE
GLY H:41 , CYS H:42 , SER H:43 , GLY H:45 , GLU H:46 , CYS H:47 , GLY H:48 , CYS H:50 , CYS H:62
BINDING SITE FOR RESIDUE FES H 908
[
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
(3, 6)
Info
All PROSITE Patterns/Profiles
1: FAD_PCMH (C:1-179,G:1-179)
2: 2FE2S_FER_2 (D:4-80,H:4-80)
3: 2FE2S_FER_1 (D:42-50,H:42-50)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
FAD_PCMH
PS51387
PCMH-type FAD-binding domain profile.
NDFS_EUBBA
1-179
2
C:1-179
G:1-179
2
2FE2S_FER_2
PS51085
2Fe-2S ferredoxin-type iron-sulfur binding domain profile.
NDSFS_EUBBA
4-80
2
D:4-80
H:4-80
3
2FE2S_FER_1
PS00197
2Fe-2S ferredoxin-type iron-sulfur binding region signature.
NDSFS_EUBBA
42-50
2
D:42-50
H:42-50
[
close PROSITE info
]
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_d3hrdd2 (D:83-160)
1b: SCOP_d3hrdh2 (H:83-157)
2a: SCOP_d3hrdd1 (D:1-82)
2b: SCOP_d3hrdh1 (H:1-82)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
CO dehydrogenase ISP C-domain like
(45)
Superfamily
:
CO dehydrogenase ISP C-domain like
(45)
Family
:
automated matches
(3)
Protein domain
:
automated matches
(3)
Eubacterium barkeri [TaxId: 1528]
(1)
1a
d3hrdd2
D:83-160
1b
d3hrdh2
H:83-157
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
beta-Grasp (ubiquitin-like)
(1032)
Superfamily
:
2Fe-2S ferredoxin-like
(174)
Family
:
automated matches
(18)
Protein domain
:
automated matches
(18)
Eubacterium barkeri [TaxId: 1528]
(1)
2a
d3hrdd1
D:1-82
2b
d3hrdh1
H:1-82
[
close SCOP info
]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_3hrdD01 (D:1-79)
1b: CATH_3hrdH01 (H:1-79)
2a: CATH_3hrdD02 (D:80-160)
2b: CATH_3hrdH02 (H:80-157)
View:
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Classes
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Architectures
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)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Roll
(3276)
Topology
:
Ubiquitin-like (UB roll)
(674)
Homologous Superfamily
:
[code=3.10.20.30, no name defined]
(153)
Clostridium barkeri (Eubacterium barkeri)
(1)
1a
3hrdD01
D:1-79
1b
3hrdH01
H:1-79
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
DNA polymerase; domain 1
(617)
Homologous Superfamily
:
[code=1.10.150.120, no name defined]
(29)
Clostridium barkeri (Eubacterium barkeri)
(1)
2a
3hrdD02
D:80-160
2b
3hrdH02
H:80-157
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Sorry, no Info available
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Atom Selection
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Protein & NOT Variant
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Protein & NOT PROSITE
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Chain C
Chain D
Chain E
Chain F
Chain G
Chain H
Asymmetric Unit 1
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