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1NMO
Asym. Unit
Info
Asym.Unit (250 KB)
Biol.Unit 1 (241 KB)
Biol.Unit 2 (242 KB)
Biol.Unit 3 (240 KB)
Biol.Unit 4 (245 KB)
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(1)
Title
:
STRUCTURAL GENOMICS, PROTEIN YBGI, 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: C,D (3x)
Biol. Unit 3: A,B (3x)
Biol. Unit 4: E,F (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
(2, 36)
Info
All Hetero Components
1a: FE (III) ION (FEa)
1b: FE (III) ION (FEb)
1c: FE (III) ION (FEc)
1d: FE (III) ION (FEd)
1e: FE (III) ION (FEe)
1f: FE (III) ION (FEf)
1g: FE (III) ION (FEg)
1h: FE (III) ION (FEh)
1i: FE (III) ION (FEi)
1j: FE (III) ION (FEj)
1k: FE (III) ION (FEk)
1l: FE (III) ION (FEl)
2a: SELENOMETHIONINE (MSEa)
2b: SELENOMETHIONINE (MSEb)
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)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FE
12
Ligand/Ion
FE (III) ION
2
MSE
24
Mod. Amino Acid
SELENOMETHIONINE
[
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Sites
(12, 12)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:64 , HIS A:215 , GLU A:219 , FE A:302
BINDING SITE FOR RESIDUE FE A 301
02
AC2
SOFTWARE
HIS A:63 , ASP A:101 , GLU A:219 , FE A:301 , HOH A:409
BINDING SITE FOR RESIDUE FE A 302
03
AC3
SOFTWARE
HIS B:64 , HIS B:215 , GLU B:219 , FE B:302
BINDING SITE FOR RESIDUE FE B 301
04
AC4
SOFTWARE
HIS B:63 , ASP B:101 , GLU B:219 , FE B:301 , HOH B:483
BINDING SITE FOR RESIDUE FE B 302
05
AC5
SOFTWARE
HIS C:64 , HIS C:215 , GLU C:219 , FE C:302
BINDING SITE FOR RESIDUE FE C 301
06
AC6
SOFTWARE
HIS C:63 , ASP C:101 , GLU C:219 , FE C:301 , HOH C:644
BINDING SITE FOR RESIDUE FE C 302
07
AC7
SOFTWARE
HIS D:64 , HIS D:215 , GLU D:219 , FE D:302
BINDING SITE FOR RESIDUE FE D 301
08
AC8
SOFTWARE
HIS D:63 , ASP D:101 , GLU D:219 , FE D:301 , HOH D:865
BINDING SITE FOR RESIDUE FE D 302
09
AC9
SOFTWARE
HIS E:64 , HIS E:215 , GLU E:219 , FE E:302
BINDING SITE FOR RESIDUE FE E 301
10
BC1
SOFTWARE
HIS E:63 , ASP E:101 , GLU E:219 , FE E:301 , HOH E:694
BINDING SITE FOR RESIDUE FE E 302
11
BC2
SOFTWARE
HIS F:64 , HIS F:215 , GLU F:219 , FE F:302
BINDING SITE FOR RESIDUE FE F 301
12
BC3
SOFTWARE
HIS F:63 , ASP F:101 , GLU F:219 , FE F:301 , HOH F:866
BINDING SITE FOR RESIDUE FE F 302
[
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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
(0, 0)
Info
All PROSITE Patterns/Profiles
;
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End label:
Sorry, no Info available
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
View:
Label:
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_d1nmoa_ (A:)
1b: SCOP_d1nmob_ (B:)
1c: SCOP_d1nmoc_ (C:)
1d: SCOP_d1nmod_ (D:)
1e: SCOP_d1nmoe_ (E:)
1f: SCOP_d1nmof_ (F:)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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
d1nmoa_
A:
1b
d1nmob_
B:
1c
d1nmoc_
C:
1d
d1nmod_
D:
1e
d1nmoe_
E:
1f
d1nmof_
F:
[
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CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_1nmoA01 (A:2-96,A:219-241)
1b: CATH_1nmoE01 (E:2-96,E:219-241)
1c: CATH_1nmoF01 (F:2-96,F:219-241)
1d: CATH_1nmoB01 (B:2-96,B:219-241)
1e: CATH_1nmoC01 (C:2-96,C:219-241)
1f: CATH_1nmoD01 (D:2-96,D:219-241)
View:
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)
Homologous Superfamilies
(
)
(
)
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
1nmoA01
A:2-96,A:219-241
1b
1nmoE01
E:2-96,E:219-241
1c
1nmoF01
F:2-96,F:219-241
1d
1nmoB01
B:2-96,B:219-241
1e
1nmoC01
C:2-96,C:219-241
1f
1nmoD01
D:2-96,D:219-241
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Chain C
Chain D
Chain E
Chain F
Asymmetric Unit 1
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select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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select non-helix/non-sheet protein parts
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Asym.Unit (250 KB)
Header - Asym.Unit
Biol.Unit 1 (241 KB)
Header - Biol.Unit 1
Biol.Unit 2 (242 KB)
Header - Biol.Unit 2
Biol.Unit 3 (240 KB)
Header - Biol.Unit 3
Biol.Unit 4 (245 KB)
Header - Biol.Unit 4
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