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2PMB
Asym. Unit
Info
Asym.Unit (307 KB)
Biol.Unit 1 (295 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF PREDICTED NUCLEOTIDE-BINDING PROTEIN FROM VIBRIO CHOLERAE
Authors
:
Y. Patskovsky, C. Zhan, W. Shi, R. Toro, J. M. Sauder, J. Gilmore, M. Iizu M. Maletic, T. Gheyi, S. R. Wasserman, D. Smith, S. K. Burley, S. C. Almo Sgx Research Center For Structural Genomics (Nysgxrc)
Date
:
20 Apr 07 (Deposition) - 08 May 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.99
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Structural Genomics, Psi, Protein Structure Initiative, New York Structural Genomics Research Consortium, Nysgrc, New York Sgx Research Center For Structural Genomics, Nysgxrc, Unknown Function
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Patskovsky, C. Zhan, W. Shi, J. M. Sauder, J. Gilmore, M. Iizuka, M. Maletic, T. Gheyi, S. R. Wasserman, D. Smith, S. K. Burley, S. C. Almo
Crystal Structure Of Predicted Nucleotide-Binding Protein From Vibrio Cholerae.
To Be Published
[
close entry info
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Hetero Components
(3, 82)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
2a: SELENOMETHIONINE (MSEa)
2aa: SELENOMETHIONINE (MSEaa)
2ab: SELENOMETHIONINE (MSEab)
2ac: SELENOMETHIONINE (MSEac)
2ad: SELENOMETHIONINE (MSEad)
2ae: SELENOMETHIONINE (MSEae)
2af: SELENOMETHIONINE (MSEaf)
2ag: SELENOMETHIONINE (MSEag)
2ah: SELENOMETHIONINE (MSEah)
2ai: SELENOMETHIONINE (MSEai)
2aj: SELENOMETHIONINE (MSEaj)
2ak: SELENOMETHIONINE (MSEak)
2al: SELENOMETHIONINE (MSEal)
2am: SELENOMETHIONINE (MSEam)
2an: SELENOMETHIONINE (MSEan)
2ao: SELENOMETHIONINE (MSEao)
2ap: SELENOMETHIONINE (MSEap)
2aq: SELENOMETHIONINE (MSEaq)
2ar: SELENOMETHIONINE (MSEar)
2as: SELENOMETHIONINE (MSEas)
2at: SELENOMETHIONINE (MSEat)
2au: SELENOMETHIONINE (MSEau)
2av: SELENOMETHIONINE (MSEav)
2aw: SELENOMETHIONINE (MSEaw)
2ax: SELENOMETHIONINE (MSEax)
2ay: SELENOMETHIONINE (MSEay)
2az: SELENOMETHIONINE (MSEaz)
2b: SELENOMETHIONINE (MSEb)
2ba: SELENOMETHIONINE (MSEba)
2bb: SELENOMETHIONINE (MSEbb)
2bc: SELENOMETHIONINE (MSEbc)
2bd: SELENOMETHIONINE (MSEbd)
2be: SELENOMETHIONINE (MSEbe)
2bf: SELENOMETHIONINE (MSEbf)
2bg: SELENOMETHIONINE (MSEbg)
2bh: SELENOMETHIONINE (MSEbh)
2bi: SELENOMETHIONINE (MSEbi)
2bj: SELENOMETHIONINE (MSEbj)
2bk: SELENOMETHIONINE (MSEbk)
2bl: SELENOMETHIONINE (MSEbl)
2bm: SELENOMETHIONINE (MSEbm)
2bn: SELENOMETHIONINE (MSEbn)
2bo: SELENOMETHIONINE (MSEbo)
2bp: SELENOMETHIONINE (MSEbp)
2c: SELENOMETHIONINE (MSEc)
2d: SELENOMETHIONINE (MSEd)
2e: SELENOMETHIONINE (MSEe)
2f: SELENOMETHIONINE (MSEf)
2g: SELENOMETHIONINE (MSEg)
2h: SELENOMETHIONINE (MSEh)
2i: SELENOMETHIONINE (MSEi)
2j: SELENOMETHIONINE (MSEj)
2k: SELENOMETHIONINE (MSEk)
2l: SELENOMETHIONINE (MSEl)
2m: SELENOMETHIONINE (MSEm)
2n: SELENOMETHIONINE (MSEn)
2o: SELENOMETHIONINE (MSEo)
2p: SELENOMETHIONINE (MSEp)
2q: SELENOMETHIONINE (MSEq)
2r: SELENOMETHIONINE (MSEr)
2s: SELENOMETHIONINE (MSEs)
2t: SELENOMETHIONINE (MSEt)
2u: SELENOMETHIONINE (MSEu)
2v: SELENOMETHIONINE (MSEv)
2w: SELENOMETHIONINE (MSEw)
2x: SELENOMETHIONINE (MSEx)
2y: SELENOMETHIONINE (MSEy)
2z: SELENOMETHIONINE (MSEz)
3a: PHOSPHATE ION (PO4a)
3b: PHOSPHATE ION (PO4b)
3c: PHOSPHATE ION (PO4c)
3d: PHOSPHATE ION (PO4d)
3e: PHOSPHATE ION (PO4e)
3f: PHOSPHATE ION (PO4f)
3g: PHOSPHATE ION (PO4g)
3h: PHOSPHATE ION (PO4h)
3i: PHOSPHATE ION (PO4i)
3j: PHOSPHATE ION (PO4j)
3k: PHOSPHATE ION (PO4k)
3l: PHOSPHATE ION (PO4l)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
2
Ligand/Ion
GLYCEROL
2
MSE
68
Mod. Amino Acid
SELENOMETHIONINE
3
PO4
12
Ligand/Ion
PHOSPHATE ION
[
close Hetero Component info
]
Sites
(14, 14)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY D:158 , HIS D:159 , GLY D:260 , PRO D:261 , GLY D:262 , THR D:263 , HOH D:611 , HOH D:688 , HOH D:719 , HOH D:720
BINDING SITE FOR RESIDUE PO4 D 601
02
AC2
SOFTWARE
LYS B:205 , GLU D:193 , LYS D:197 , ASN D:228
BINDING SITE FOR RESIDUE PO4 D 602
03
AC3
SOFTWARE
GLY B:158 , HIS B:159 , GLY B:260 , PRO B:261 , GLY B:262 , THR B:263 , HOH B:707 , HOH B:844
BINDING SITE FOR RESIDUE PO4 B 603
04
AC4
SOFTWARE
GLY A:158 , HIS A:159 , GLY A:260 , PRO A:261 , GLY A:262 , THR A:263 , HOH A:679 , HOH A:735
BINDING SITE FOR RESIDUE PO4 A 604
05
AC5
SOFTWARE
GLY C:158 , HIS C:159 , GLY C:260 , PRO C:261 , GLY C:262 , THR C:263 , HOH C:715 , HOH C:799
BINDING SITE FOR RESIDUE PO4 C 605
06
AC6
SOFTWARE
GLU A:74 , ARG A:75 , ARG D:339 , LYS D:343 , TYR D:349
BINDING SITE FOR RESIDUE PO4 D 606
07
AC7
SOFTWARE
PRO B:285 , ILE B:286 , HIS B:316 , TYR B:317 , SER B:318 , HOH B:841
BINDING SITE FOR RESIDUE PO4 B 607
08
AC8
SOFTWARE
LYS A:205 , GLU C:193 , LYS C:197 , ASN C:228
BINDING SITE FOR RESIDUE PO4 C 608
09
AC9
SOFTWARE
ARG B:339 , LYS B:343 , TYR B:349 , GLU C:74 , ARG C:75
BINDING SITE FOR RESIDUE PO4 B 609
10
BC1
SOFTWARE
ARG A:339 , LYS A:343 , TYR A:349 , HOH C:771 , ARG D:75
BINDING SITE FOR RESIDUE PO4 A 610
11
BC2
SOFTWARE
ARG B:75 , ARG C:339 , LYS C:343 , TYR C:349
BINDING SITE FOR RESIDUE PO4 C 611
12
BC3
SOFTWARE
GLU B:193 , LYS B:197 , ASN B:228 , LYS D:205
BINDING SITE FOR RESIDUE PO4 B 612
13
BC4
SOFTWARE
ALA C:127 , THR C:131 , ARG C:249 , LEU C:355 , LYS C:356 , ILE C:357
BINDING SITE FOR RESIDUE GOL C 701
14
BC5
SOFTWARE
MSE B:16 , ASP B:17 , ARG B:107 , TYR B:111 , ASN B:140 , ARG C:139
BINDING SITE FOR RESIDUE GOL B 702
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
End label:
Sorry, no Info available
[
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]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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
(0, 0)
Info
All SCOP Domains
View:
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Label:
Sorry, no Info available
[
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CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_2pmbA01 (A:5-116)
1b: CATH_2pmbB01 (B:5-116)
1c: CATH_2pmbD01 (D:5-117)
1d: CATH_2pmbC01 (C:5-116)
2a: CATH_2pmbA02 (A:126-455)
2b: CATH_2pmbB02 (B:126-455)
2c: CATH_2pmbC02 (C:126-455)
2d: CATH_2pmbD02 (D:126-455)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
MCP/YpsA-like
(3)
Homologous Superfamily
:
MoCo carrier protein-like
(3)
Vibrio cholerae. Organism_taxid: 666. Strain: el tor inaba n16961.
(1)
1a
2pmbA01
A:5-116
1b
2pmbB01
B:5-116
1c
2pmbD01
D:5-117
1d
2pmbC01
C:5-116
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.450, no name defined]
(19)
Vibrio cholerae. Organism_taxid: 666. Strain: el tor inaba n16961.
(1)
2a
2pmbA02
A:126-455
2b
2pmbB02
B:126-455
2c
2pmbC02
C:126-455
2d
2pmbD02
D:126-455
[
close CATH info
]
Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_Lysine_decarbox_2pmbD01 (D:192-331)
1b: PFAM_Lysine_decarbox_2pmbD02 (D:192-331)
1c: PFAM_Lysine_decarbox_2pmbD03 (D:192-331)
1d: PFAM_Lysine_decarbox_2pmbD04 (D:192-331)
2a: PFAM_DUF3412_2pmbD05 (D:334-456)
2b: PFAM_DUF3412_2pmbD06 (D:334-456)
2c: PFAM_DUF3412_2pmbD07 (D:334-456)
2d: PFAM_DUF3412_2pmbD08 (D:334-456)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
DprA
(10)
Family
:
Lysine_decarbox
(8)
Vibrio cholerae
(1)
1a
Lysine_decarbox-2pmbD01
D:192-331
1b
Lysine_decarbox-2pmbD02
D:192-331
1c
Lysine_decarbox-2pmbD03
D:192-331
1d
Lysine_decarbox-2pmbD04
D:192-331
Clan
:
no clan defined [family: DUF3412]
(1)
Family
:
DUF3412
(1)
Vibrio cholerae
(1)
2a
DUF3412-2pmbD05
D:334-456
2b
DUF3412-2pmbD06
D:334-456
2c
DUF3412-2pmbD07
D:334-456
2d
DUF3412-2pmbD08
D:334-456
[
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]
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