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2I14
Asym. Unit
Info
Asym.Unit (382 KB)
Biol.Unit 1 (374 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF NICOTINATE-NUCLEOTIDE PYROPHOSPHORYLASE FROM PYROCOCCUS FURIOSUS
Authors
:
D. H. Shin, R. Kim, S. -H. Kim, Berkeley Structural Genomics Center (Bsgc)
Date
:
12 Aug 06 (Deposition) - 10 Oct 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.90
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Nicotinate-Nucleotide Pyrophosphorylase, Crystal Structure, Ligand Binding, Phosphoribosylpyrophosphate, Zn Metal Ion, Structural Genomics, Psi, Protein Structure Initiative, Berkeley Structural Genomics Center, Bsgc, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
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Reference
:
D. H. Shin, R. Kim, S. -H. Kim, R. Pufan, H. Yokota
Crystal Structure Of Nicotinate-Nucleotide Pyrophosphorylase From Pyrococcus Furiosus
To Be Published
(for further references see the
PDB file header
)
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Hetero Components
(2, 18)
Info
All Hetero Components
1a: 1-ALPHA-PYROPHOSPHORYL-2-ALPHA,3-A... (PCPa)
1b: 1-ALPHA-PYROPHOSPHORYL-2-ALPHA,3-A... (PCPb)
1c: 1-ALPHA-PYROPHOSPHORYL-2-ALPHA,3-A... (PCPc)
1d: 1-ALPHA-PYROPHOSPHORYL-2-ALPHA,3-A... (PCPd)
1e: 1-ALPHA-PYROPHOSPHORYL-2-ALPHA,3-A... (PCPe)
1f: 1-ALPHA-PYROPHOSPHORYL-2-ALPHA,3-A... (PCPf)
2a: ZINC ION (ZNa)
2b: ZINC ION (ZNb)
2c: ZINC ION (ZNc)
2d: ZINC ION (ZNd)
2e: ZINC ION (ZNe)
2f: ZINC ION (ZNf)
2g: ZINC ION (ZNg)
2h: ZINC ION (ZNh)
2i: ZINC ION (ZNi)
2j: ZINC ION (ZNj)
2k: ZINC ION (ZNk)
2l: ZINC ION (ZNl)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
PCP
6
Ligand/Ion
1-ALPHA-PYROPHOSPHORYL-2-ALPHA,3-ALPHA-DIHYDROXY-4-BETA-CYCLOPENTANE-METHANOL-5-PHOSPHATE
2
ZN
12
Ligand/Ion
ZINC ION
[
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Sites
(18, 18)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
CYS A:327 , HIS A:331 , CYS A:344 , VAL A:346 , CYS A:347
BINDING SITE FOR RESIDUE ZN A 391
02
AC2
SOFTWARE
HIS A:178 , ASP A:209 , ASP A:235
BINDING SITE FOR RESIDUE ZN A 393
03
AC3
SOFTWARE
CYS B:727 , HIS B:731 , CYS B:744 , VAL B:746 , CYS B:747
BINDING SITE FOR RESIDUE ZN B 791
04
AC4
SOFTWARE
HIS B:578 , ASP B:609 , ASP B:635
BINDING SITE FOR RESIDUE ZN B 793
05
AC5
SOFTWARE
CYS C:1327 , HIS C:1331 , CYS C:1344 , VAL C:1346 , CYS C:1347
BINDING SITE FOR RESIDUE ZN C 1391
06
AC6
SOFTWARE
HIS C:1178 , ASP C:1209 , ASP C:1235
BINDING SITE FOR RESIDUE ZN C 1393
07
AC7
SOFTWARE
CYS D:1727 , HIS D:1731 , CYS D:1744 , VAL D:1746 , CYS D:1747
BINDING SITE FOR RESIDUE ZN D 1791
08
AC8
SOFTWARE
HIS D:1578 , ASP D:1609 , ASP D:1635
BINDING SITE FOR RESIDUE ZN D 1793
09
AC9
SOFTWARE
CYS E:2327 , HIS E:2331 , CYS E:2344 , VAL E:2346 , CYS E:2347
BINDING SITE FOR RESIDUE ZN E 2391
10
BC1
SOFTWARE
HIS E:2178 , ASP E:2209 , ASP E:2235
BINDING SITE FOR RESIDUE ZN E 2393
11
BC2
SOFTWARE
CYS F:2727 , HIS F:2731 , CYS F:2744 , VAL F:2746 , CYS F:2747
BINDING SITE FOR RESIDUE ZN F 2791
12
BC3
SOFTWARE
HIS F:2578 , ASP F:2609 , ASP F:2635
BINDING SITE FOR RESIDUE ZN F 2793
13
BC4
SOFTWARE
PHE A:134 , ARG A:137 , HIS A:138 , PRO A:177 , HIS A:178 , ARG A:233 , ASP A:235 , GLY A:270 , GLY A:289 , GLY A:290 , TYR B:421
BINDING SITE FOR RESIDUE PCP A 392
14
BC5
SOFTWARE
TYR A:21 , HOH B:1 , PHE B:534 , ARG B:537 , HIS B:538 , PRO B:577 , HIS B:578 , ARG B:633 , ASP B:635 , GLY B:670 , GLY B:689 , GLY B:690
BINDING SITE FOR RESIDUE PCP B 792
15
BC6
SOFTWARE
PHE C:1134 , ARG C:1137 , HIS C:1138 , PRO C:1177 , HIS C:1178 , ARG C:1233 , ASP C:1235 , GLY C:1270 , GLY C:1289 , GLY C:1290 , TYR D:1421
BINDING SITE FOR RESIDUE PCP C 1392
16
BC7
SOFTWARE
TYR C:1021 , HOH D:3 , PHE D:1534 , ARG D:1537 , HIS D:1538 , PRO D:1577 , HIS D:1578 , ARG D:1633 , ASP D:1635 , GLY D:1670 , GLY D:1689 , GLY D:1690
BINDING SITE FOR RESIDUE PCP D 1792
17
BC8
SOFTWARE
HOH E:7 , PHE E:2134 , ARG E:2137 , HIS E:2138 , PRO E:2177 , HIS E:2178 , ARG E:2233 , ASP E:2235 , GLY E:2270 , GLY E:2289 , GLY E:2290 , TYR F:2421
BINDING SITE FOR RESIDUE PCP E 2392
18
BC9
SOFTWARE
TYR E:2021 , HOH F:2 , PHE F:2534 , ARG F:2537 , HIS F:2538 , PRO F:2577 , HIS F:2578 , ARG F:2633 , ASP F:2635 , GLY F:2670 , GLY F:2689 , GLY F:2690
BINDING SITE FOR RESIDUE PCP F 2792
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
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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, 12)
Info
All SCOP Domains
1a: SCOP_d2i14a2 (A:1-110)
1b: SCOP_d2i14b2 (B:401-510)
1c: SCOP_d2i14c2 (C:1001-1110)
1d: SCOP_d2i14d2 (D:1401-1510)
1e: SCOP_d2i14e2 (E:2001-2110)
1f: SCOP_d2i14f2 (F:2401-2510)
2a: SCOP_d2i14a1 (A:111-389)
2b: SCOP_d2i14b1 (B:511-789)
2c: SCOP_d2i14c1 (C:1111-1389)
2d: SCOP_d2i14d1 (D:1511-1789)
2e: SCOP_d2i14e1 (E:2111-2389)
2f: SCOP_d2i14f1 (F:2511-2789)
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)
(
)
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(
)
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(
)
(
)
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(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
alpha/beta-Hammerhead
(191)
Superfamily
:
Nicotinate/Quinolinate PRTase N-terminal domain-like
(25)
Family
:
NadC N-terminal domain-like
(13)
Protein domain
:
Nicotinate-nucleotide pyrophosphorylase PF1904
(1)
Pyrococcus furiosus [TaxId: 2261]
(1)
1a
d2i14a2
A:1-110
1b
d2i14b2
B:401-510
1c
d2i14c2
C:1001-1110
1d
d2i14d2
D:1401-1510
1e
d2i14e2
E:2001-2110
1f
d2i14f2
F:2401-2510
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Nicotinate/Quinolinate PRTase C-terminal domain-like
(25)
Family
:
NadC C-terminal domain-like
(13)
Protein domain
:
Nicotinate-nucleotide pyrophosphorylase PF1904
(1)
Pyrococcus furiosus [TaxId: 2261]
(1)
2a
d2i14a1
A:111-389
2b
d2i14b1
B:511-789
2c
d2i14c1
C:1111-1389
2d
d2i14d1
D:1511-1789
2e
d2i14e1
E:2111-2389
2f
d2i14f1
F:2511-2789
[
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CATH Domains
(2, 12)
Info
all CATH domains
1a: CATH_2i14A02 (A:107-297)
1b: CATH_2i14B02 (B:507-697)
1c: CATH_2i14C02 (C:1107-1297)
1d: CATH_2i14D02 (D:1507-1697)
1e: CATH_2i14E02 (E:2107-2297)
1f: CATH_2i14F02 (F:2507-2697)
2a: CATH_2i14A01 (A:1-106)
2b: CATH_2i14B01 (B:401-506)
2c: CATH_2i14C01 (C:1001-1106)
2d: CATH_2i14D01 (D:1401-1506)
2e: CATH_2i14E01 (E:2001-2106)
2f: CATH_2i14F01 (F:2401-2506)
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)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Aldolase class I
(887)
Pyrococcus furiosus. Organism_taxid: 2261.
(11)
1a
2i14A02
A:107-297
1b
2i14B02
B:507-697
1c
2i14C02
C:1107-1297
1d
2i14D02
D:1507-1697
1e
2i14E02
E:2107-2297
1f
2i14F02
F:2507-2697
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Aldehyde Oxidoreductase; domain 3
(111)
Homologous Superfamily
:
[code=3.90.1170.20, no name defined]
(12)
Pyrococcus furiosus. Organism_taxid: 2261.
(1)
2a
2i14A01
A:1-106
2b
2i14B01
B:401-506
2c
2i14C01
C:1001-1106
2d
2i14D01
D:1401-1506
2e
2i14E01
E:2001-2106
2f
2i14F01
F:2401-2506
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Pfam Domains
(0, 0)
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