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1R27
Biol. Unit 4
Info
Asym.Unit (597 KB)
Biol.Unit 1 (300 KB)
Biol.Unit 2 (299 KB)
Biol.Unit 3, α-C (2.3 MB)
Biol.Unit 3 (2.3 MB)
Biol.Unit 4, α-C (1.1 MB)
Biol.Unit 4 (1.1 MB)
Biol.Unit 5 (587 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF NARGH COMPLEX
Authors
:
M. Jormakka, D. Richardson, B. Byrne, S. Iwata
Date
:
26 Sep 03 (Deposition) - 17 Feb 04 (Release) - 31 Mar 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: A,B,C,D (4x)
Biol. Unit 4: A,B,C,D (2x)
Biol. Unit 5: A,B,C,D (1x)
Keywords
:
Beta Barrel; X-Ray Crystallography, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Jormakka, D. Richardson, B. Byrne, S. Iwata
Architecture Of Nargh Reveals A Structural Classification Of Mo-Bismgd Enzymes
Structure V. 12 95 2004
(for further references see the
PDB file header
)
[
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Hetero Components
(3, 14)
Info
All Hetero Components
1a: FE3-S4 CLUSTER (F3Sa)
1b: FE3-S4 CLUSTER (F3Sb)
2a: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,... (MGDa)
2b: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,... (MGDb)
2c: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,... (MGDc)
2d: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,... (MGDd)
3a: MOLYBDENUM ATOM (MOa)
3b: MOLYBDENUM ATOM (MOb)
4a: IRON/SULFUR CLUSTER (SF4a)
4b: IRON/SULFUR CLUSTER (SF4b)
4c: IRON/SULFUR CLUSTER (SF4c)
4d: IRON/SULFUR CLUSTER (SF4d)
4e: IRON/SULFUR CLUSTER (SF4e)
4f: IRON/SULFUR CLUSTER (SF4f)
4g: IRON/SULFUR CLUSTER (SF4g)
4h: IRON/SULFUR CLUSTER (SF4h)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
F3S
2
Ligand/Ion
FE3-S4 CLUSTER
2
MGD
4
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
8
Ligand/Ion
IRON/SULFUR CLUSTER
[
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Sites
(16, 16)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:222 , MGD A:5801 , MGD A:5802 , HOH A:6570
BINDING SITE FOR RESIDUE MO A 5803
02
AC2
SOFTWARE
ASP C:222 , MGD C:7801 , MGD C:7802 , HOH C:8538
BINDING SITE FOR RESIDUE MO C 7803
03
AC3
SOFTWARE
CYS B:196 , ILE B:201 , CYS B:217 , ARG B:218 , TRP B:220 , ARG B:221 , MET B:222 , CYS B:223 , SER B:241
BINDING SITE FOR RESIDUE F3S B 5808
04
AC4
SOFTWARE
CYS D:196 , ILE D:201 , CYS D:217 , ARG D:218 , TRP D:220 , ARG D:221 , MET D:222 , CYS D:223 , SER D:241
BINDING SITE FOR RESIDUE F3S D 7808
05
AC5
SOFTWARE
CYS B:26 , ASN B:42 , CYS B:244 , ILE B:245 , PHE B:246 , CYS B:247 , THR B:257 , CYS B:259
BINDING SITE FOR RESIDUE SF4 B 5800
06
AC6
SOFTWARE
CYS B:184 , GLU B:185 , CYS B:187 , ALA B:191 , CYS B:192 , CYS B:227 , TYR B:229 , ILE B:232 , LYS B:243
BINDING SITE FOR RESIDUE SF4 B 5805
07
AC7
SOFTWARE
CYS B:16 , GLY B:18 , CYS B:19 , HIS B:20 , CYS B:22 , CYS B:263 , GLY B:265 , ILE B:267 , ARG B:268
BINDING SITE FOR RESIDUE SF4 B 5806
08
AC8
SOFTWARE
HIS A:49 , VAL A:51 , CYS A:53 , GLY A:55 , SER A:56 , CYS A:57 , TRP A:59 , GLY A:91 , CYS A:92 , TYR A:1101
BINDING SITE FOR RESIDUE SF4 A 5807
09
AC9
SOFTWARE
CYS D:26 , TRP D:30 , ASN D:42 , CYS D:244 , ILE D:245 , PHE D:246 , CYS D:247 , THR D:257 , CYS D:259
BINDING SITE FOR RESIDUE SF4 D 7800
10
BC1
SOFTWARE
CYS D:184 , GLU D:185 , CYS D:187 , ALA D:191 , CYS D:192 , CYS D:227 , TYR D:229 , ILE D:232 , LYS D:243
BINDING SITE FOR RESIDUE SF4 D 7805
11
BC2
SOFTWARE
CYS D:16 , CYS D:19 , HIS D:20 , CYS D:22 , CYS D:263 , VAL D:264 , GLY D:265 , ILE D:267 , ARG D:268
BINDING SITE FOR RESIDUE SF4 D 7806
12
BC3
SOFTWARE
HIS C:49 , VAL C:51 , CYS C:53 , GLY C:55 , SER C:56 , CYS C:57 , TRP C:59 , GLY C:91 , CYS C:92 , GLY C:95 , TYR C:1101
BINDING SITE FOR RESIDUE SF4 C 7807
13
BC4
SOFTWARE
GLY A:50 , ASN A:52 , PRO A:190 , TYR A:220 , ASP A:222 , HIS A:546 , TRP A:712 , ARG A:713 , SER A:714 , ASN A:715 , SER A:720 , LYS A:722 , LEU A:771 , ASP A:772 , PHE A:773 , ARG A:774 , THR A:788 , TRP A:791 , LYS A:794 , ASP A:822 , THR A:1090 , HIS A:1092 , ILE A:1097 , HIS A:1098 , SER A:1099 , THR A:1100 , HIS A:1163 , ASN A:1185 , ASN A:1217 , ARG A:1218 , MGD A:5802 , MO A:5803 , HOH A:5995 , HOH A:6018 , HOH A:6058 , HOH A:6090 , HOH A:6135 , HOH A:6568 , HOH A:6570 , HOH A:6580
BINDING SITE FOR RESIDUE MGD A 5801
14
BC5
SOFTWARE
ASN A:52 , ARG A:94 , ASP A:222 , TRP A:252 , GLY A:253 , ASN A:255 , GLN A:258 , THR A:259 , VAL A:280 , THR A:281 , PRO A:282 , ASP A:283 , ALA A:285 , GLN A:299 , GLY A:300 , ASP A:302 , GLY A:541 , ALA A:542 , GLY A:543 , LEU A:544 , TRP A:547 , TYR A:577 , VAL A:578 , GLY A:579 , PRO A:1091 , HIS A:1092 , GLN A:1093 , GLY A:1096 , ILE A:1097 , HIS A:1098 , ARG A:1218 , MGD A:5801 , MO A:5803 , HOH A:5875 , HOH A:5889 , HOH A:5923 , HOH A:6075 , HOH A:6577 , HOH A:6615
BINDING SITE FOR RESIDUE MGD A 5802
15
BC6
SOFTWARE
GLY C:50 , ASN C:52 , PRO C:190 , TYR C:220 , ASP C:222 , HIS C:546 , ARG C:713 , SER C:714 , ASN C:715 , SER C:720 , LYS C:722 , LEU C:771 , ASP C:772 , PHE C:773 , ARG C:774 , THR C:788 , TRP C:791 , LYS C:794 , ASP C:822 , THR C:1090 , HIS C:1092 , ILE C:1097 , HIS C:1098 , SER C:1099 , THR C:1100 , HIS C:1163 , HIS C:1184 , ASN C:1185 , ASN C:1217 , ARG C:1218 , MGD C:7802 , MO C:7803 , HOH C:7861 , HOH C:7908 , HOH C:8037 , HOH C:8108 , HOH C:8538 , HOH C:8539
BINDING SITE FOR RESIDUE MGD C 7801
16
BC7
SOFTWARE
ASN C:52 , ARG C:94 , ASP C:222 , TRP C:252 , GLY C:253 , ASN C:255 , GLN C:258 , THR C:259 , VAL C:280 , THR C:281 , PRO C:282 , ASP C:283 , ALA C:285 , GLN C:299 , GLY C:300 , ASP C:302 , GLY C:541 , ALA C:542 , GLY C:543 , LEU C:544 , TRP C:547 , TYR C:577 , VAL C:578 , GLY C:579 , PRO C:1091 , HIS C:1092 , GLN C:1093 , GLY C:1096 , ILE C:1097 , HIS C:1098 , ARG C:1218 , MGD C:7801 , MO C:7803 , HOH C:7833 , HOH C:7865 , HOH C:7970 , HOH C:8022 , HOH C:8129
BINDING SITE FOR RESIDUE MGD C 7802
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(5, 28)
Info
All PROSITE Patterns/Profiles
1: 4FE4S_FER_2 (B:7-35,D:208-237)
2: 4FE4S_MOW_BIS_MGD (A:42-106,C:42-106)
3: MOLYBDOPTERIN_PROK_1 (A:47-65,C:47-65)
4: MOLYBDOPTERIN_PROK_2 (A:776-793,C:776-793)
5: MOLYBDOPTERIN_PROK_3 (A:1124-1151,C:1124-1151)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
4FE4S_FER_2
PS51379
4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
NARH_ECOLI
7-35
175-206
208-237
12
B:7-35
D:7-35
B:175-206
D:175-206
B:208-237
D:208-237
2
4FE4S_MOW_BIS_MGD
PS51669
Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile.
NARG_ECOLI
43-107
4
A:42-106
C:42-106
3
MOLYBDOPTERIN_PROK_1
PS00551
Prokaryotic molybdopterin oxidoreductases signature 1.
NARG_ECOLI
48-66
4
A:47-65
C:47-65
4
MOLYBDOPTERIN_PROK_2
PS00490
Prokaryotic molybdopterin oxidoreductases signature 2.
NARG_ECOLI
777-794
4
A:776-793
C:776-793
5
MOLYBDOPTERIN_PROK_3
PS00932
Prokaryotic molybdopterin oxidoreductases signature 3.
NARG_ECOLI
1125-1152
4
A:1124-1151
C:1124-1151
[
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(3, 6)
Info
All SCOP Domains
1a: SCOP_d1r27a1 (A:1075-1246)
1b: SCOP_d1r27c1 (C:1075-1246)
2a: SCOP_d1r27b_ (B:)
2b: SCOP_d1r27d_ (D:)
3a: SCOP_d1r27a2 (A:29-1074)
3b: SCOP_d1r27c2 (C:29-1074)
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(
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)
(
)
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
:
Respiratory nitrate reductase 1 alpha chain
(7)
Escherichia coli [TaxId: 562]
(7)
1a
d1r27a1
A:1075-1246
1b
d1r27c1
C:1075-1246
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ferredoxin-like
(1795)
Superfamily
:
4Fe-4S ferredoxins
(143)
Family
:
Ferredoxin domains from multidomain proteins
(69)
Protein domain
:
Respiratory nitrate reductase 1 beta chain
(11)
Escherichia coli [TaxId: 562]
(8)
2a
d1r27b_
B:
2b
d1r27d_
D:
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
:
Respiratory nitrate reductase 1 alpha chain
(7)
Escherichia coli [TaxId: 562]
(7)
3a
d1r27a2
A:29-1074
3b
d1r27c2
C:29-1074
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
[
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Pfam Domains
(3, 6)
Info
all PFAM domains
1a: PFAM_Fer4_11_1r27D01 (D:175-273)
1b: PFAM_Fer4_11_1r27D02 (D:175-273)
2a: PFAM_Molydop_binding_1r27C01 (C:1086-1205)
2b: PFAM_Molydop_binding_1r27C02 (C:1086-1205)
3a: PFAM_Molybdopterin_1r27C03 (C:107-832)
3b: PFAM_Molybdopterin_1r27C04 (C:107-832)
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Clans
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)
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(
)
Organisms
(
)
(
)
Clan
:
4Fe-4S
(51)
Family
:
Fer4_11
(12)
Escherichia coli (strain K12)
(8)
1a
Fer4_11-1r27D01
D:175-273
1b
Fer4_11-1r27D02
D:175-273
Clan
:
AcetylDC-like
(37)
Family
:
Molydop_binding
(24)
Escherichia coli (strain K12)
(9)
2a
Molydop_binding-1r27C01
C:1086-1205
2b
Molydop_binding-1r27C02
C:1086-1205
Clan
:
no clan defined [family: Molybdopterin]
(24)
Family
:
Molybdopterin
(24)
Escherichia coli (strain K12)
(9)
3a
Molybdopterin-1r27C03
C:107-832
3b
Molybdopterin-1r27C04
C:107-832
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