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1YH8
Asym. Unit
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Asym.Unit (96 KB)
Biol.Unit 1 (92 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF AQUIFEX AEOLICUS LPXC DEACETYLASE COMPLEXED WITH PALMITATE
Authors
:
M. Hernick, H. A. Gennadios, D. A. Whittington, K. M. Rusche, D. W. Christianson, C. A. Fierke
Date
:
07 Jan 05 (Deposition) - 15 Feb 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
X-Ray Crystallography; A. Aeolicus, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Hernick, H. A. Gennadios, D. A. Whittington, K. M. Rusche, D. W. Christianson, C. A. Fierke
Udp-3-O-((R)-3-Hydroxymyristoyl)-N- Acetylglucosamine Deacetylase Functions Through A General Acid-Base Catalyst Pair Mechanism
J. Biol. Chem. V. 280 16969 2005
(for further references see the
PDB file header
)
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Hetero Components
(3, 10)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
2a: PALMITOLEIC ACID (PAMa)
2b: PALMITOLEIC ACID (PAMb)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
3c: ZINC ION (ZNc)
3d: ZINC ION (ZNd)
3e: ZINC ION (ZNe)
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Label:
No.
Name
Count
Type
Full Name
1
CL
3
Ligand/Ion
CHLORIDE ION
2
PAM
2
Ligand/Ion
PALMITOLEIC ACID
3
ZN
5
Ligand/Ion
ZINC ION
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Sites
(10, 10)
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)
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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:79 , HIS A:238 , ASP A:242 , PAM A:801
BINDING SITE FOR RESIDUE ZN A 501
02
AC2
SOFTWARE
HIS A:58 , HIS A:200
BINDING SITE FOR RESIDUE ZN A 503
03
AC3
SOFTWARE
ILE A:27 , HIS A:29 , GLU A:95 , GLY B:2 , GLU B:126
BINDING SITE FOR RESIDUE ZN A 504
04
AC4
SOFTWARE
HIS B:79 , HIS B:238 , ASP B:242 , PAM B:802
BINDING SITE FOR RESIDUE ZN B 505
05
AC5
SOFTWARE
HIS B:58 , HIS B:200 , CL B:603 , HOH B:863
BINDING SITE FOR RESIDUE ZN B 507
06
AC6
SOFTWARE
HIS A:79 , ILE A:103 , SER A:107
BINDING SITE FOR RESIDUE CL A 601
07
AC7
SOFTWARE
GLY B:15 , VAL B:16 , ILE B:103 , LEU B:104
BINDING SITE FOR RESIDUE CL B 602
08
AC8
SOFTWARE
HIS B:58 , HIS B:200 , ZN B:507
BINDING SITE FOR RESIDUE CL B 603
09
AC9
SOFTWARE
ILE A:18 , HIS A:58 , GLU A:78 , HIS A:79 , THR A:191 , GLY A:210 , HIS A:238 , ASP A:242 , HIS A:265 , ZN A:501
BINDING SITE FOR RESIDUE PAM A 801
10
BC1
SOFTWARE
LEU A:212 , ILE B:18 , HIS B:58 , GLU B:78 , HIS B:79 , THR B:191 , SER B:211 , HIS B:238 , ASP B:242 , HIS B:265 , ZN B:505
BINDING SITE FOR RESIDUE PAM B 802
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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
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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, 4)
Info
All SCOP Domains
1a: SCOP_d1yh8a1 (A:2-127)
1b: SCOP_d1yh8a2 (A:128-279)
1c: SCOP_d1yh8b1 (B:2-127)
1d: SCOP_d1yh8b2 (B:128-279)
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Protein Domains
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)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ribosomal protein S5 domain 2-like
(306)
Superfamily
:
Ribosomal protein S5 domain 2-like
(306)
Family
:
UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase LpxC
(13)
Protein domain
:
UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase LpxC
(10)
Aquifex aeolicus [TaxId: 63363]
(10)
1a
d1yh8a1
A:2-127
1b
d1yh8a2
A:128-279
1c
d1yh8b1
B:2-127
1d
d1yh8b2
B:128-279
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1yh8A02 (A:129-279)
1b: CATH_1yh8B02 (B:129-279)
2a: CATH_1yh8A01 (A:2-128)
2b: CATH_1yh8B01 (B:2-128)
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)
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)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
lpxc deacetylase, domain 1
(11)
Homologous Superfamily
:
lpxc deacetylase, domain 2
(11)
Aquifex aeolicus. Organism_taxid: 63363.
(10)
1a
1yh8A02
A:129-279
1b
1yh8B02
B:129-279
Topology
:
Ribosomal Protein S5; domain 2
(189)
Homologous Superfamily
:
lpxc deacetylase, domain 1
(11)
Aquifex aeolicus. Organism_taxid: 63363.
(10)
2a
1yh8A01
A:2-128
2b
1yh8B01
B:2-128
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Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_LpxC_1yh8B01 (B:2-279)
1b: PFAM_LpxC_1yh8B02 (B:2-279)
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Clan
:
S5
(103)
Family
:
LpxC
(10)
Aquifex aeolicus
(8)
1a
LpxC-1yh8B01
B:2-279
1b
LpxC-1yh8B02
B:2-279
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Asymmetric Unit 1
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