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3IC1
Biol. Unit 1
Info
Asym.Unit (126 KB)
Biol.Unit 1 (121 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF ZINC-BOUND SUCCINYL-DIAMINOPIMELATE DESUCCINYLASE FROM HAEMOPHILUS INFLUENZAE
Authors
:
B. P. Nocek, D. M. Gillner, R. C. Holz, A. Joachimiak, Midwest Center F Structural Genomics (Mcsg)
Date
:
17 Jul 09 (Deposition) - 22 Sep 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Dape, Psi2, Mcsg, Zn Bound, Succinyl-Diaminopimelate Desuccinylase, Structural Genomics, Protein Structure Initiative, Midwest Center For Structural Genomics, Amino-Acid Biosynthesis, Cobalt, Diaminopimelate Biosynthesis, Hydrolase, Lysine Biosynthesis, Metal- Binding
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. P. Nocek, D. M. Gillner, Y. Fan, R. C. Holz, A. Joachimiak
Structural Basis For Catalysis By The Mono- And Dimetalated Forms Of The Dape-Encoded N-Succinyl-L, L-Diaminopimelic Aci Desuccinylase.
J. Mol. Biol. V. 397 617 2010
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Hetero Components
(2, 7)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
2d: SULFATE ION (SO4d)
2e: SULFATE ION (SO4e)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
3c: ZINC ION (ZNc)
3d: ZINC ION (ZNd)
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Label:
No.
Name
Count
Type
Full Name
1
GOL
2
Ligand/Ion
GLYCEROL
2
SO4
5
Ligand/Ion
SULFATE ION
3
ZN
-1
Ligand/Ion
ZINC 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:67 , ASP A:100 , GLU A:134 , GLU A:135 , GLU A:163 , HOH A:482 , ZN A:1002
BINDING SITE FOR RESIDUE ZN A 1001
02
AC2
SOFTWARE
ASP A:100 , GLU A:135 , HIS A:349 , HOH A:482 , ZN A:1001
BINDING SITE FOR RESIDUE ZN A 1002
03
AC3
SOFTWARE
LYS A:269 , TRP A:287
BINDING SITE FOR RESIDUE GOL A 3002
04
AC4
SOFTWARE
ARG A:178 , ARG A:179 , ARG A:258 , GLY A:322 , GLY A:323 , GLY A:324 , HOH A:397
BINDING SITE FOR RESIDUE SO4 A 378
05
AC5
SOFTWARE
GLY A:299 , LYS A:300 , HOH A:380 , GLU B:87 , HOH B:458
BINDING SITE FOR RESIDUE SO4 A 379
06
AC6
SOFTWARE
LEU B:344 , SER B:356 , ASP B:359
BINDING SITE FOR RESIDUE GOL B 3001
07
AC7
SOFTWARE
ARG B:258 , THR B:325 , ARG B:329 , HOH B:445
BINDING SITE FOR RESIDUE SO4 B 378
08
AC8
SOFTWARE
GLY B:323 , GLY B:324
BINDING SITE FOR RESIDUE SO4 B 379
09
AC9
SOFTWARE
ARG B:178 , ARG B:179 , ARG B:258 , GLY B:322 , HOH B:390 , HOH B:466
BINDING SITE FOR RESIDUE SO4 B 380
10
BC1
SOFTWARE
ASP B:100 , GLU B:135 , HIS B:349 , HOH B:479 , ZN B:1001
BINDING SITE FOR RESIDUE ZN B 1002
11
BC2
SOFTWARE
HIS B:67 , ASP B:100 , GLU B:134 , GLU B:163 , HOH B:479 , ZN B:1002
BINDING SITE FOR RESIDUE ZN B 1001
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: ARGE_DAPE_CPG2_1 (A:62-71,B:62-71)
2: ARGE_DAPE_CPG2_2 (A:98-137,B:98-137)
;
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PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ARGE_DAPE_CPG2_1
PS00758
ArgE / dapE / ACY1 / CPG2 / yscS family signature 1.
DAPE_HAEIN
62-71
2
A:62-71
B:62-71
2
ARGE_DAPE_CPG2_2
PS00759
ArgE / dapE / ACY1 / CPG2 / yscS family signature 2.
DAPE_HAEIN
98-137
2
A:98-137
B:98-137
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Exons
(0, 0)
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All Exons
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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SCOP Domains
(0, 0)
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_3ic1A02 (A:179-292)
1b: CATH_3ic1B02 (B:179-292)
2a: CATH_3ic1A01 (A:1-178,A:293-376)
2b: CATH_3ic1B01 (B:1-178,B:293-376)
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(
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(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Alpha-Beta Plaits
(1688)
Homologous Superfamily
:
[code=3.30.70.360, no name defined]
(23)
Haemophilus influenzae. Organism_taxid: 727.
(1)
1a
3ic1A02
A:179-292
1b
3ic1B02
B:179-292
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Aminopeptidase
(284)
Homologous Superfamily
:
Zn peptidases
(137)
Haemophilus influenzae. Organism_taxid: 727.
(1)
2a
3ic1A01
A:1-178,A:293-376
2b
3ic1B01
B:1-178,B:293-376
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Pfam Domains
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Asymmetric Unit 1
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