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2NAP
Asym. Unit
Info
Asym.Unit (134 KB)
Biol.Unit 1 (129 KB)
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(1)
Title
:
DISSIMILATORY NITRATE REDUCTASE (NAP) FROM DESULFOVIBRIO DESULFURICANS
Authors
:
J. M. Dias, M. Than, A. Humm, R. Huber, G. Bourenkov, H. Bartunik, S. Bursakov, J. Calvete, J. Caldeira, C. Carneiro, J. Moura, I. Moura, M. J. Romao
Date
:
18 Sep 98 (Deposition) - 19 Sep 99 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Nitrogenous Acceptor, Dissimilatory Nitrate Reductase, Crystal Structure, Multiwavelength Anomalous Diffraction, Molybdopterin Cofactor, [4Fe-4S] Cluster, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. M. Dias, M. E. Than, A. Humm, R. Huber, G. P. Bourenkov, H. D. Bartunik, S. Bursakov, J. Calvete, J. Caldeira, C. Carneiro, J. J. Moura, I. Moura, M. J. Romao
Crystal Structure Of The First Dissimilatory Nitrate Reductase At 1. 9 A Solved By Mad Methods.
Structure Fold. Des. V. 7 65 1999
(for further references see the
PDB file header
)
[
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Hetero Components
(4, 5)
Info
All Hetero Components
1a: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESa)
2a: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,... (MGDa)
2b: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,... (MGDb)
3a: MOLYBDENUM ATOM (MOa)
4a: IRON/SULFUR CLUSTER (SF4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MES
1
Ligand/Ion
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
2
MGD
2
Ligand/Ion
2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINEDINUCLEOTIDE
3
MO
1
Ligand/Ion
MOLYBDENUM ATOM
4
SF4
1
Ligand/Ion
IRON/SULFUR CLUSTER
[
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]
Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: FS4 (AUTHOR)
7: MGD (AUTHOR)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
CYS A:13 , TYR A:15 , CYS A:16 , GLY A:19 , CYS A:20 , CYS A:47 , VAL A:183
BINDING SITE FOR RESIDUE SF4 A 800
2
AC2
SOFTWARE
CYS A:140 , MGD A:811 , MGD A:812 , HOH A:813
BINDING SITE FOR RESIDUE MO A 810
3
AC3
SOFTWARE
ARG A:14 , GLN A:111 , ASN A:136 , CYS A:140 , GLN A:312 , GLU A:416 , THR A:417 , ASN A:418 , THR A:422 , ILE A:443 , GLU A:444 , ALA A:445 , PHE A:446 , ALA A:449 , PRO A:461 , ALA A:462 , PHE A:463 , SER A:615 , ARG A:617 , TRP A:622 , HIS A:623 , THR A:624 , THR A:626 , MET A:627 , PHE A:689 , ASN A:697 , TYR A:713 , LYS A:714 , MO A:810 , MGD A:812 , HOH A:1181 , HOH A:1249 , HOH A:1507
BINDING SITE FOR RESIDUE MGD A 811
4
AC4
SOFTWARE
CYS A:16 , LYS A:49 , CYS A:140 , ILE A:173 , GLY A:174 , SER A:175 , ASN A:176 , GLU A:179 , ALA A:180 , ASP A:204 , PRO A:205 , ARG A:206 , PHE A:220 , PRO A:222 , GLY A:223 , ASP A:225 , CYS A:307 , MET A:308 , GLY A:309 , ARG A:313 , GLY A:345 , THR A:614 , MET A:616 , ARG A:617 , VAL A:618 , ILE A:619 , HIS A:621 , TRP A:622 , HIS A:623 , LYS A:714 , MO A:810 , MGD A:811 , HOH A:1074 , HOH A:1099 , HOH A:1150 , HOH A:1251
BINDING SITE FOR RESIDUE MGD A 812
5
AC5
SOFTWARE
ALA A:142 , VAL A:145 , GLY A:146 , VAL A:149 , THR A:150 , HIS A:361 , VAL A:707 , SER A:708 , HOH A:1096 , HOH A:1276 , HOH A:1347 , HOH A:1456 , HOH A:1542
BINDING SITE FOR RESIDUE MES A 2300
6
FS4
AUTHOR
SF4 A:800
4 IRON - 4 SULFUR CLUSTER
7
MGD
AUTHOR
MO A:810 , MGD A:811 , MGD A:812
MOLYBDOPTERIN GUANINE DINUCLEOTIDE COFACTOR
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: 4FE4S_MOW_BIS_MGD (A:6-61)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
4FE4S_MOW_BIS_MGD
PS51669
Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile.
NAPA_DESDA
38-93
1
A:6-61
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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.
SCOP Domains
(2, 2)
Info
All SCOP Domains
1a: SCOP_d2napa1 (A:601-723)
2a: SCOP_d2napa2 (A:4-600)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Double psi beta-barrel
(111)
Superfamily
:
ADC-like
(88)
Family
:
Formate dehydrogenase/DMSO reductase, C-terminal domain
(41)
Protein domain
:
Periplasmic nitrate reductase alpha chain, NapA
(6)
Desulfovibrio desulfuricans [TaxId: 876]
(5)
1a
d2napa1
A:601-723
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Formate dehydrogenase/DMSO reductase, domains 1-3
(53)
Superfamily
:
Formate dehydrogenase/DMSO reductase, domains 1-3
(53)
Family
:
Formate dehydrogenase/DMSO reductase, domains 1-3
(53)
Protein domain
:
Periplasmic nitrate reductase alpha chain
(6)
Desulfovibrio desulfuricans [TaxId: 876]
(5)
2a
d2napa2
A:4-600
[
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CATH Domains
(4, 4)
Info
all CATH domains
1a: CATH_2napA03 (A:140-345,A:563-594)
2a: CATH_2napA02 (A:62-139,A:346-562)
3a: CATH_2napA04 (A:610-723)
4a: CATH_2napA01 (A:4-61)
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)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Dimethylsulfoxide Reductase; domain 2
(37)
Homologous Superfamily
:
Dimethylsulfoxide Reductase, domain 2
(37)
Desulfovibrio desulfuricans. Organism_taxid: 876.
(8)
1a
2napA03
A:140-345,A:563-594
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.740, no name defined]
(37)
Desulfovibrio desulfuricans. Organism_taxid: 876.
(8)
2a
2napA02
A:62-139,A:346-562
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Barwin-like endoglucanases
(75)
Homologous Superfamily
:
[code=2.40.40.20, no name defined]
(63)
Desulfovibrio desulfuricans. Organism_taxid: 876.
(8)
3a
2napA04
A:610-723
Architecture
:
Single Sheet
(341)
Topology
:
N-terminal domain of TfIIb
(166)
Homologous Superfamily
:
ADC-like domains
(18)
Desulfovibrio desulfuricans. Organism_taxid: 876.
(8)
4a
2napA01
A:4-61
[
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]
Pfam Domains
(0, 0)
Info
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Chain A
Asymmetric Unit 1
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Asym.Unit (134 KB)
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