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1QY9
Asym. Unit
Info
Asym.Unit (204 KB)
Biol.Unit 1 (100 KB)
Biol.Unit 2 (101 KB)
Biol.Unit 3 (196 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF E. COLI SE-MET PROTEIN YDDE
Authors
:
A. Grassick, G. Sulzenbacher, V. Roig-Zamboni, V. Campanacci, C. Camb Y. Bourne
Date
:
10 Sep 03 (Deposition) - 08 Jun 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.05
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: A,B,C,D (1x)
Keywords
:
Putative Phenazine Biosynthesis Protein; Epimerase; Antibiotic Biosynthesis Protein; Structural Genomics, Unknown Function
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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Reference
:
A. Grassick, G. Sulzenbacher, V. Roig-Zamboni, V. Campanacci, C. Cambillau, Y. Bourne
Crystal Structure Of E. Coli Ydde Protein Reveals A Strikin Homology With Diaminopimelate Epimerase
Proteins V. 55 764 2004
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Hetero Components
(3, 25)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
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)
3a: HYDROXIDE ION (OHa)
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Label:
No.
Name
Count
Type
Full Name
1
GOL
3
Ligand/Ion
GLYCEROL
2
MSE
21
Mod. Amino Acid
SELENOMETHIONINE
3
OH
1
Ligand/Ion
HYDROXIDE ION
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
CYS B:72 , GLY B:73
BINDING SITE FOR RESIDUE OH B 9072
2
AC2
SOFTWARE
CYS A:72 , GLY A:73 , HIS A:161 , LYS A:163 , THR A:225 , GLY A:226 , ASN A:227
BINDING SITE FOR RESIDUE GOL A 1000
3
AC3
SOFTWARE
CYS D:72 , GLY D:73 , HIS D:161 , LYS D:163 , THR D:225 , GLY D:226 , ASN D:227
BINDING SITE FOR RESIDUE GOL D 2000
4
AC4
SOFTWARE
ALA A:100 , GLY A:101 , LYS A:102 , HOH A:3056 , GLU D:32 , GLN D:36 , HOH D:2038
BINDING SITE FOR RESIDUE GOL A 3000
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SAPs(SNPs)/Variants
(0, 0)
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(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
(1, 8)
Info
All SCOP Domains
1a: SCOP_d1qy9a1 (A:3-129)
1b: SCOP_d1qy9a2 (A:130-297)
1c: SCOP_d1qy9b1 (B:3-129)
1d: SCOP_d1qy9b2 (B:130-297)
1e: SCOP_d1qy9c1 (C:2-129)
1f: SCOP_d1qy9c2 (C:130-297)
1g: SCOP_d1qy9d1 (D:1-129)
1h: SCOP_d1qy9d2 (D:130-297)
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Diaminopimelate epimerase-like
(37)
Superfamily
:
Diaminopimelate epimerase-like
(37)
Family
:
PhzC/PhzF-like
(11)
Protein domain
:
Hypothetical protein YddE
(3)
Escherichia coli [TaxId: 562]
(3)
1a
d1qy9a1
A:3-129
1b
d1qy9a2
A:130-297
1c
d1qy9b1
B:3-129
1d
d1qy9b2
B:130-297
1e
d1qy9c1
C:2-129
1f
d1qy9c2
C:130-297
1g
d1qy9d1
D:1-129
1h
d1qy9d2
D:130-297
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CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_1qy9C01 (C:2-121,C:285-297)
1b: CATH_1qy9D02 (D:122-284)
1c: CATH_1qy9D01 (D:2-121,D:285-297)
1d: CATH_1qy9A01 (A:3-121,A:285-297)
1e: CATH_1qy9B01 (B:3-121,B:285-297)
1f: CATH_1qy9A02 (A:122-284)
1g: CATH_1qy9B02 (B:122-284)
1h: CATH_1qy9C02 (C:122-284)
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Homologous Superfamilies
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)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Roll
(3276)
Topology
:
Diaminopimelate Epimerase; Chain A, domain 1
(22)
Homologous Superfamily
:
Diaminopimelate Epimerase; Chain A, domain 1
(22)
Escherichia coli. Organism_taxid: 562.
(3)
1a
1qy9C01
C:2-121,C:285-297
1b
1qy9D02
D:122-284
1c
1qy9D01
D:2-121,D:285-297
1d
1qy9A01
A:3-121,A:285-297
1e
1qy9B01
B:3-121,B:285-297
1f
1qy9A02
A:122-284
1g
1qy9B02
B:122-284
1h
1qy9C02
C:122-284
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_PhzC_PhzF_1qy9D01 (D:8-291)
1b: PFAM_PhzC_PhzF_1qy9D02 (D:8-291)
1c: PFAM_PhzC_PhzF_1qy9D03 (D:8-291)
1d: PFAM_PhzC_PhzF_1qy9D04 (D:8-291)
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Clan
:
DAP_epimerase
(14)
Family
:
PhzC-PhzF
(10)
Escherichia coli (strain K12)
(3)
1a
PhzC-PhzF-1qy9D01
D:8-291
1b
PhzC-PhzF-1qy9D02
D:8-291
1c
PhzC-PhzF-1qy9D03
D:8-291
1d
PhzC-PhzF-1qy9D04
D:8-291
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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 (204 KB)
Header - Asym.Unit
Biol.Unit 1 (100 KB)
Header - Biol.Unit 1
Biol.Unit 2 (101 KB)
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Biol.Unit 3 (196 KB)
Header - Biol.Unit 3
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