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1NMO
Biol. Unit 1
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
(1, 24)
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
-1
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 only available for the asymmetric unit)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(, 0)
Info
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;
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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
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Label:
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
(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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Classes
(
)
(
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Architectures
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Topologies
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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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Protein & NOT Site
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Chain A
Chain B
Chain C
Chain D
Chain E
Chain F
Asymmetric Unit 1
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select chains 'A' and 'C'
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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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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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