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1NMP
Asym. Unit
Info
Asym.Unit (246 KB)
Biol.Unit 1 (239 KB)
Biol.Unit 2 (243 KB)
Biol.Unit 3 (237 KB)
Biol.Unit 4 (239 KB)
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(1)
Title
:
STRUCTURAL GENOMICS, YBGI PROTEIN, UNKNOWN FUNCTION
Authors
:
J. E. Ladner, G. Obmolova, A. Teplyakov, P. P. Khil, R. D. Camerini-Oter G. L. Gilliland, Structure 2 Function Project (S2F)
Date
:
10 Jan 03 (Deposition) - 20 Jan 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Biol. Unit 2: E,F (3x)
Biol. Unit 3: A,B (3x)
Biol. Unit 4: C,D (3x)
Keywords
:
Ybgi, Hypothetical Protein, Toroidal Structure, Structure 2 Function Project, S2F, Structural Genomics, Unknown Function
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. E. Ladner, G. Obmolova, A. Teplyakov, A. J. Howard, P. P. Khil, R. D. Camerini-Otero, G. L. Gilliland
Crystal Structure Of Escherichia Coli Protein Ybgi, A Toroidal Structure With A Dinuclear Metal Site
Bmc Struct. Biol. V. 3 7 2003
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Hetero Components
(1, 11)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
1c: MAGNESIUM ION (MGc)
1d: MAGNESIUM ION (MGd)
1e: MAGNESIUM ION (MGe)
1f: MAGNESIUM ION (MGf)
1g: MAGNESIUM ION (MGg)
1h: MAGNESIUM ION (MGh)
1i: MAGNESIUM ION (MGi)
1j: MAGNESIUM ION (MGj)
1k: MAGNESIUM ION (MGk)
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No.
Name
Count
Type
Full Name
1
MG
11
Ligand/Ion
MAGNESIUM ION
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Sites
(11, 11)
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)
View:
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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:63 , HIS A:64 , HIS A:215 , GLU A:219 , MG A:302 , HOH A:367
BINDING SITE FOR RESIDUE MG A 301
02
AC2
SOFTWARE
HIS A:63 , ASP A:101 , GLU A:219 , MG A:301
BINDING SITE FOR RESIDUE MG A 302
03
AC3
SOFTWARE
HIS B:63 , ASP B:101 , GLU B:219 , HOH B:380
BINDING SITE FOR RESIDUE MG B 302
04
AC4
SOFTWARE
HIS C:64 , HIS C:215 , GLU C:219 , MG C:302
BINDING SITE FOR RESIDUE MG C 301
05
AC5
SOFTWARE
HIS C:63 , ASP C:101 , GLU C:219 , MG C:301 , HOH C:356
BINDING SITE FOR RESIDUE MG C 302
06
AC6
SOFTWARE
HIS D:63 , HIS D:64 , HIS D:215 , GLU D:219 , MG D:302
BINDING SITE FOR RESIDUE MG D 301
07
AC7
SOFTWARE
HIS D:63 , ASP D:101 , GLU D:219 , MG D:301 , HOH D:338
BINDING SITE FOR RESIDUE MG D 302
08
AC8
SOFTWARE
HIS E:63 , HIS E:64 , HIS E:215 , GLU E:219 , MG E:302
BINDING SITE FOR RESIDUE MG E 301
09
AC9
SOFTWARE
HIS E:63 , ASP E:101 , GLU E:219 , MG E:301 , HOH E:357
BINDING SITE FOR RESIDUE MG E 302
10
BC1
SOFTWARE
HIS F:63 , HIS F:64 , HIS F:215 , GLU F:219 , MG F:302 , HOH F:499
BINDING SITE FOR RESIDUE MG F 301
11
BC2
SOFTWARE
HIS F:63 , ASP F:101 , GLU F:219 , MG F:301 , HOH F:335
BINDING SITE FOR RESIDUE MG F 302
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
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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
(1, 6)
Info
All SCOP Domains
1a: SCOP_d1nmpa_ (A:)
1b: SCOP_d1nmpe_ (E:)
1c: SCOP_d1nmpf_ (F:)
1d: SCOP_d1nmpb_ (B:)
1e: SCOP_d1nmpc_ (C:)
1f: SCOP_d1nmpd_ (D:)
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
NIF3 (NGG1p interacting factor 3)-like
(9)
Superfamily
:
NIF3 (NGG1p interacting factor 3)-like
(9)
Family
:
NIF3 (NGG1p interacting factor 3)-like
(4)
Protein domain
:
Hypothetical protein YbgI
(2)
Escherichia coli [TaxId: 562]
(2)
1a
d1nmpa_
A:
1b
d1nmpe_
E:
1c
d1nmpf_
F:
1d
d1nmpb_
B:
1e
d1nmpc_
C:
1f
d1nmpd_
D:
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CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_1nmpA01 (A:1-96,A:219-241)
1b: CATH_1nmpB01 (B:1-96,B:219-241)
1c: CATH_1nmpC01 (C:1-96,C:219-241)
1d: CATH_1nmpD01 (D:1-96,D:219-241)
1e: CATH_1nmpE01 (E:1-96,E:219-241)
1f: CATH_1nmpF01 (F:1-96,F:219-241)
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Homologous Superfamilies
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(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
(9)
Homologous Superfamily
:
NIF3 (NGG1p interacting factor 3)-like
(4)
Escherichia coli, escherichia coli o157:h7. ,. Organism_taxid: 562,83334. Strain: , o157:h7.
(2)
1a
1nmpA01
A:1-96,A:219-241
1b
1nmpB01
B:1-96,B:219-241
1c
1nmpC01
C:1-96,C:219-241
1d
1nmpD01
D:1-96,D:219-241
1e
1nmpE01
E:1-96,E:219-241
1f
1nmpF01
F:1-96,F:219-241
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Pfam Domains
(0, 0)
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Asymmetric Unit 1
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Show PDB file:
Asym.Unit (246 KB)
Header - Asym.Unit
Biol.Unit 1 (239 KB)
Header - Biol.Unit 1
Biol.Unit 2 (243 KB)
Header - Biol.Unit 2
Biol.Unit 3 (237 KB)
Header - Biol.Unit 3
Biol.Unit 4 (239 KB)
Header - Biol.Unit 4
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