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5D29
Asym. Unit
Info
Asym.Unit (263 KB)
Biol.Unit 1 (507 KB)
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(1)
Title
:
X-RAY STRUCTURE OF HUMAN GLUTAMATE CARBOXYPEPTIDASE II (GCPII) IN COMPLEX WITH A HYDROXAMATE INHIBITOR JHU241
Authors
:
C. Barinka, Z. Novakova, J. Pavlicek
Date
:
05 Aug 15 (Deposition) - 27 Apr 16 (Release) - 08 Jun 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A
Biol. Unit 1: A (2x)
Keywords
:
Prostate-Specific Membrane Antigen, Naaladase, Phosphoramidate, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Z. Novakova, K. Wozniak, A. Jancarik, R. Rais, Y. Wu, J. Pavlicek, D. Ferraris, B. Havlinova, J. Ptacek, J. Vavra, N. Hin, C. Rojas, P. Majer, B. S. Slusher, T. Tsukamoto, C. Barinka
Unprecedented Binding Mode Of Hydroxamate-Based Inhibitors Of Glutamate Carboxypeptidase Ii: Structural Characterization And Biological Activity.
J. Med. Chem. V. 59 4539 2016
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Hetero Components
(7, 18)
Info
All Hetero Components
1a: 4-[(2~{S})-2-CARBOXY-5-(OXIDANYLAM... (5Q1a)
2a: ACETATE ION (ACTa)
3a: BETA-D-MANNOSE (BMAa)
3b: BETA-D-MANNOSE (BMAb)
4a: CALCIUM ION (CAa)
5a: CHLORIDE ION (CLa)
6a: N-ACETYL-D-GLUCOSAMINE (NAGa)
6b: N-ACETYL-D-GLUCOSAMINE (NAGb)
6c: N-ACETYL-D-GLUCOSAMINE (NAGc)
6d: N-ACETYL-D-GLUCOSAMINE (NAGd)
6e: N-ACETYL-D-GLUCOSAMINE (NAGe)
6f: N-ACETYL-D-GLUCOSAMINE (NAGf)
6g: N-ACETYL-D-GLUCOSAMINE (NAGg)
6h: N-ACETYL-D-GLUCOSAMINE (NAGh)
6i: N-ACETYL-D-GLUCOSAMINE (NAGi)
6j: N-ACETYL-D-GLUCOSAMINE (NAGj)
7a: ZINC ION (ZNa)
7b: ZINC ION (ZNb)
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No.
Name
Count
Type
Full Name
1
5Q1
1
Ligand/Ion
4-[(2~{S})-2-CARBOXY-5-(OXIDANYLAMINO)-5-OXIDANYLIDENE-PENTYL]BENZOIC ACID
2
ACT
1
Ligand/Ion
ACETATE ION
3
BMA
2
Ligand/Ion
BETA-D-MANNOSE
4
CA
1
Ligand/Ion
CALCIUM ION
5
CL
1
Ligand/Ion
CHLORIDE ION
6
NAG
10
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
7
ZN
2
Ligand/Ion
ZINC ION
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Sites
(13, 13)
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: AD1 (SOFTWARE)
11: AD2 (SOFTWARE)
12: AD3 (SOFTWARE)
13: AD4 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:387 , GLU A:425 , HIS A:553 , ZN A:814 , 5Q1 A:818
binding site for residue ZN A 813
02
AC2
SOFTWARE
HIS A:377 , ASP A:387 , ASP A:453 , ZN A:813 , 5Q1 A:818 , HOH A:974
binding site for residue ZN A 814
03
AC3
SOFTWARE
THR A:269 , TYR A:272 , GLU A:433 , GLU A:436 , HOH A:962
binding site for residue CA A 815
04
AC4
SOFTWARE
ASN A:451 , ASP A:453 , ARG A:534 , ARG A:536
binding site for residue CL A 816
05
AC5
SOFTWARE
PHE A:209 , ARG A:210 , GLU A:425 , TYR A:552 , HIS A:553 , TYR A:700 , 5Q1 A:818 , HOH A:918
binding site for residue ACT A 817
06
AC6
SOFTWARE
TYR A:234 , HIS A:377 , ASP A:387 , GLU A:424 , GLU A:425 , ASP A:453 , GLY A:518 , ASN A:519 , ARG A:534 , ARG A:536 , GLY A:548 , TYR A:549 , TYR A:552 , HIS A:553 , TYR A:700 , ZN A:813 , ZN A:814 , ACT A:817 , HOH A:920 , HOH A:926 , HOH A:974
binding site for residue 5Q1 A 818
07
AC7
SOFTWARE
ASN A:76 , GLN A:95 , GLN A:99 , HOH A:1077
binding site for Poly-Saccharide residues NAG A 801 through NAG A 802 bound to ASN A 76
08
AC8
SOFTWARE
ASN A:121 , THR A:123 , HIS A:124 , THR A:349
binding site for Mono-Saccharide NAG A 803 bound to ASN A 121
09
AC9
SOFTWARE
TYR A:127 , GLU A:137 , ILE A:138 , ASN A:140
binding site for Mono-Saccharide NAG A 804 bound to ASN A 140
10
AD1
SOFTWARE
ASN A:195 , SER A:197
binding site for Mono-Saccharide NAG A 805 bound to ASN A 195
11
AD2
SOFTWARE
TRP A:246 , ASN A:459 , PHE A:565 , TYR A:566 , HOH A:991 , HOH A:1079 , HOH A:1107
binding site for Mono-Saccharide NAG A 806 bound to ASN A 459
12
AD3
SOFTWARE
SER A:472 , ASN A:476 , PRO A:594 , HOH A:1187
binding site for Poly-Saccharide residues NAG A 807 through NAG A 808 bound to ASN A 476
13
AD4
SOFTWARE
HIS A:112 , SER A:241 , GLU A:276 , TYR A:277 , LYS A:324 , ARG A:354 , SER A:631 , SER A:634 , ASN A:638 , GLN A:740 , HOH A:907 , HOH A:908 , HOH A:913 , HOH A:1112 , HOH A:1125 , HOH A:1192
binding site for Poly-Saccharide residues NAG A 809 through BMA A 812 bound to ASN A 638
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SAPs(SNPs)/Variants
(0, 0)
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Exons
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SCOP Domains
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CATH Domains
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Pfam Domains
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Chain A
Asymmetric Unit 1
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