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1YHC
Asym. Unit
Info
Asym.Unit (102 KB)
Biol.Unit 1 (97 KB)
Biol.Unit 2 (97 KB)
Biol.Unit 3 (51 KB)
Biol.Unit 4 (50 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF AQUIFEX AEOLICUS LPXC DEACETYLASE COMPLEXED WITH CACODYLATE
Authors
:
M. Hernick, H. A. Gennadios, D. A. Whittington, K. M. Rusche, D. W. Chris C. A. Fierke
Date
:
07 Jan 05 (Deposition) - 15 Feb 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Biol. Unit 2: A,B (1x)
Biol. Unit 3: A (1x)
Biol. Unit 4: 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
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Hetero Components
(6, 15)
Info
All Hetero Components
1a: CACODYLATE ION (CACa)
1b: CACODYLATE ION (CACb)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
3a: GLYCEROL (GOLa)
4a: PALMITOLEIC ACID (PAMa)
4b: PALMITOLEIC ACID (PAMb)
5a: SULFATE ION (SO4a)
5b: SULFATE ION (SO4b)
6a: ZINC ION (ZNa)
6b: ZINC ION (ZNb)
6c: ZINC ION (ZNc)
6d: ZINC ION (ZNd)
6e: ZINC ION (ZNe)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CAC
2
Ligand/Ion
CACODYLATE ION
2
CL
3
Ligand/Ion
CHLORIDE ION
3
GOL
1
Ligand/Ion
GLYCEROL
4
PAM
2
Ligand/Ion
PALMITOLEIC ACID
5
SO4
2
Ligand/Ion
SULFATE ION
6
ZN
5
Ligand/Ion
ZINC ION
[
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Sites
(15, 15)
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)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:79 , THR A:191 , HIS A:238 , ASP A:242 , CAC A:401
BINDING SITE FOR RESIDUE ZN A 601
02
AC2
SOFTWARE
HIS B:79 , THR B:191 , HIS B:238 , ASP B:242 , CAC B:402
BINDING SITE FOR RESIDUE ZN B 602
03
AC3
SOFTWARE
GLY A:2 , GLU A:126 , ILE B:27 , HIS B:29 , GLU B:95
BINDING SITE FOR RESIDUE ZN A 603
04
AC4
SOFTWARE
HIS A:58 , HIS A:200 , CL A:334 , CL A:336
BINDING SITE FOR RESIDUE ZN A 606
05
AC5
SOFTWARE
HIS B:58 , HIS B:200 , CL B:335 , HOH B:947
BINDING SITE FOR RESIDUE ZN B 607
06
AC6
SOFTWARE
HIS A:58 , GLU A:78 , HIS A:79 , THR A:191 , HIS A:238 , ASP A:242 , HIS A:265 , SO4 A:404 , ZN A:601 , PAM A:802
BINDING SITE FOR RESIDUE CAC A 401
07
AC7
SOFTWARE
HIS B:58 , GLU B:78 , HIS B:79 , THR B:191 , HIS B:238 , ASP B:242 , HIS B:265 , SO4 B:403 , ZN B:602 , PAM B:801
BINDING SITE FOR RESIDUE CAC B 402
08
AC8
SOFTWARE
THR B:56 , HIS B:58 , LYS B:239 , GLY B:264 , HIS B:265 , CAC B:402 , PAM B:801 , HOH B:881 , HOH B:946
BINDING SITE FOR RESIDUE SO4 B 403
09
AC9
SOFTWARE
HIS A:58 , LYS A:239 , GLY A:264 , HIS A:265 , CAC A:401 , PAM A:802 , HOH A:931 , HOH A:969
BINDING SITE FOR RESIDUE SO4 A 404
10
BC1
SOFTWARE
ASN A:57 , HIS A:58 , PHE A:167 , HIS A:200 , CL A:336 , ZN A:606
BINDING SITE FOR RESIDUE CL A 334
11
BC2
SOFTWARE
HIS B:58 , HIS B:200 , ZN B:607
BINDING SITE FOR RESIDUE CL B 335
12
BC3
SOFTWARE
HIS A:58 , HIS A:200 , CL A:334 , ZN A:606
BINDING SITE FOR RESIDUE CL A 336
13
BC4
SOFTWARE
TYR A:224 , PAM A:802 , ILE B:18 , HIS B:58 , PHE B:192 , ALA B:193 , GLU B:197 , ILE B:198 , ILE B:201 , GLY B:210 , VAL B:217 , CAC B:402 , SO4 B:403 , HOH B:827 , HOH B:939 , HOH B:940
BINDING SITE FOR RESIDUE PAM B 801
14
BC5
SOFTWARE
HIS A:19 , HIS A:58 , PHE A:192 , GLU A:197 , ILE A:198 , ILE A:201 , GLY A:210 , SER A:211 , LEU A:212 , VAL A:217 , CAC A:401 , SO4 A:404 , PAM B:801
BINDING SITE FOR RESIDUE PAM A 802
15
BC6
SOFTWARE
VAL A:53 , THR A:56 , GLU A:158 , ARG A:170 , GLN A:171 , LYS A:172 , LYS A:273 , HOH A:888
BINDING SITE FOR RESIDUE GOL A 701
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
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Exons
(0, 0)
Info
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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_d1yhca1 (A:2-127)
1b: SCOP_d1yhcb1 (B:2-127)
1c: SCOP_d1yhcb2 (B:128-279)
1d: SCOP_d1yhca2 (A:128-279)
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Protein Domains
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(
)
Organisms
(
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(
)
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
d1yhca1
A:2-127
1b
d1yhcb1
B:2-127
1c
d1yhcb2
B:128-279
1d
d1yhca2
A:128-279
[
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1yhcA02 (A:129-279)
1b: CATH_1yhcB02 (B:129-279)
2a: CATH_1yhcA01 (A:2-128)
2b: CATH_1yhcB01 (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
1yhcA02
A:129-279
1b
1yhcB02
B:129-279
Topology
:
Ribosomal Protein S5; domain 2
(189)
Homologous Superfamily
:
lpxc deacetylase, domain 1
(11)
Aquifex aeolicus. Organism_taxid: 63363.
(10)
2a
1yhcA01
A:2-128
2b
1yhcB01
B:2-128
[
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Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_LpxC_1yhcB01 (B:2-279)
1b: PFAM_LpxC_1yhcB02 (B:2-279)
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Clan
:
S5
(103)
Family
:
LpxC
(10)
Aquifex aeolicus
(8)
1a
LpxC-1yhcB01
B:2-279
1b
LpxC-1yhcB02
B:2-279
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