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3BI0
Biol. Unit 1
Info
Asym.Unit (143 KB)
Biol.Unit 1 (267 KB)
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(1)
Title
:
X-RAY STRUCTURE OF HUMAN GLUTAMATE CARBOXYPEPTIDASE II (GCPII) IN COMPLEX WITH A TRANSITION STATE ANALOG OF GLU-GLU
Authors
:
J. Lubkowski, C. Barinka
Date
:
29 Nov 07 (Deposition) - 08 Jan 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.67
Chains
:
Asym. Unit : A
Biol. Unit 1: A (2x)
Keywords
:
Prostate Specific Membrane Antigen; Metallopeptidase; Folate Hydrolase; Glutamate Carboxypeptidase Ii; Naaladase, Dipeptidase, Glycoprotein, Metal-Binding, Metalloprotease, Multifunctional Enzyme, Protease, Signal-Anchor, Transmembrane, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. Barinka, K. Hlouchova, M. Rovenska, P. Majer, M. Dauter, N. Hin, Y. S. Ko, T. Tsukamoto, B. S. Slusher, J. Konvalinka, J. Lubkowski
Structural Basis Of Interactions Between Human Glutamate Carboxypeptidase Ii And Its Substrate Analogs
J. Mol. Biol. V. 376 1438 2008
[
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Hetero Components
(4, 28)
Info
All Hetero Components
1a: (2S)-2-{[(S)-[(3S)-3-AMINO-3-CARBO... (BIXa)
2a: BETA-D-MANNOSE (BMAa)
3a: CALCIUM ION (CAa)
4a: CHLORIDE ION (CLa)
5a: ALPHA-D-MANNOSE (MANa)
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)
6k: N-ACETYL-D-GLUCOSAMINE (NAGk)
7a: ZINC ION (ZNa)
7b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BIX
2
Ligand/Ion
(2S)-2-{[(S)-[(3S)-3-AMINO-3-CARBOXYPROPYL](HYDROXY)PHOSPHORYL]METHYL}PENTANEDIOIC ACID
2
BMA
2
Ligand/Ion
BETA-D-MANNOSE
3
CA
-1
Ligand/Ion
CALCIUM ION
4
CL
-1
Ligand/Ion
CHLORIDE ION
5
MAN
2
Ligand/Ion
ALPHA-D-MANNOSE
6
NAG
22
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
7
ZN
-1
Ligand/Ion
ZINC ION
[
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Sites
(18, 18)
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)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:76 , GLN A:95 , GLN A:99 , NAG A:1756 , HOH A:2016 , HOH A:2057 , HOH A:2324
BINDING SITE FOR RESIDUE NAG A 1755
02
AC2
SOFTWARE
NAG A:1755 , HOH A:2026 , HOH A:2324 , HOH A:2375
BINDING SITE FOR RESIDUE NAG A 1756
03
AC3
SOFTWARE
ASN A:121 , THR A:123 , HIS A:124 , THR A:349 , HOH A:1984 , HOH A:2095 , HOH A:2409
BINDING SITE FOR RESIDUE NAG A 1757
04
AC4
SOFTWARE
TYR A:127 , GLU A:137 , ILE A:138 , ASN A:140 , NAG A:1767 , HOH A:2270
BINDING SITE FOR RESIDUE NAG A 1758
05
AC5
SOFTWARE
NAG A:1758 , HOH A:2179 , HOH A:2369
BINDING SITE FOR RESIDUE NAG A 1767
06
AC6
SOFTWARE
ASN A:195 , SER A:197
BINDING SITE FOR RESIDUE NAG A 1759
07
AC7
SOFTWARE
TRP A:246 , ASN A:459 , PHE A:565 , TYR A:566 , HOH A:1845 , HOH A:2044 , HOH A:2096 , HOH A:2162 , HOH A:2388
BINDING SITE FOR RESIDUE NAG A 1760
08
AC8
SOFTWARE
SER A:472 , ASN A:476 , PRO A:594 , NAG A:1762 , HOH A:2053 , HOH A:2103 , HOH A:2308
BINDING SITE FOR RESIDUE NAG A 1761
09
AC9
SOFTWARE
NAG A:1761 , HOH A:1986 , HOH A:2385
BINDING SITE FOR RESIDUE NAG A 1762
10
BC1
SOFTWARE
TYR A:277 , SER A:631 , SER A:634 , ASN A:638 , GLN A:740 , NAG A:1764 , HOH A:1894 , HOH A:1928 , HOH A:2133
BINDING SITE FOR RESIDUE NAG A 1763
11
BC2
SOFTWARE
NAG A:1763 , BMA A:1765 , HOH A:2169 , HOH A:2406
BINDING SITE FOR RESIDUE NAG A 1764
12
BC3
SOFTWARE
HIS A:112 , GLU A:276 , ARG A:354 , NAG A:1764 , MAN A:1766 , HOH A:2376 , HOH A:2377 , HOH A:2406
BINDING SITE FOR RESIDUE BMA A 1765
13
BC4
SOFTWARE
PHE A:235 , LYS A:240 , SER A:241 , GLU A:276 , BMA A:1765 , HOH A:1959 , HOH A:2131 , HOH A:2134 , HOH A:2364
BINDING SITE FOR RESIDUE MAN A 1766
14
BC5
SOFTWARE
BIX A:1 , ASP A:387 , GLU A:425 , HIS A:553 , ZN A:1752
BINDING SITE FOR RESIDUE ZN A 1751
15
BC6
SOFTWARE
BIX A:1 , HIS A:377 , ASP A:387 , GLU A:424 , ASP A:453 , ZN A:1751
BINDING SITE FOR RESIDUE ZN A 1752
16
BC7
SOFTWARE
THR A:269 , TYR A:272 , GLU A:433 , GLU A:436 , HOH A:1773
BINDING SITE FOR RESIDUE CA A 1753
17
BC8
SOFTWARE
ASN A:451 , ASP A:453 , ARG A:534 , ARG A:536 , HOH A:1788
BINDING SITE FOR RESIDUE CL A 1754
18
BC9
SOFTWARE
ARG A:210 , ASN A:257 , HIS A:377 , ASP A:387 , GLU A:424 , GLU A:425 , GLY A:427 , ASP A:453 , GLY A:518 , ASN A:519 , ARG A:534 , ARG A:536 , TYR A:552 , HIS A:553 , LYS A:699 , TYR A:700 , ZN A:1751 , ZN A:1752 , HOH A:1776 , HOH A:1939 , HOH A:1943 , HOH A:2353 , HOH A:2397
BINDING SITE FOR RESIDUE BIX A 1
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SAPs(SNPs)/Variants
(3, 6)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_024592 (Y75H, chain A, )
2: VAR_012736 (H475Y, chain A, )
3: VAR_028882 (V627L, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_024592
Y
75
H
FOLH1_HUMAN
Polymorphism
202676
A
Y
75
H
2
UniProt
VAR_012736
H
475
Y
FOLH1_HUMAN
Polymorphism
61886492
A
H
475
Y
3
UniProt
VAR_028882
V
627
L
FOLH1_HUMAN
Polymorphism
2988342
A
V
627
L
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
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Sorry, no Info available
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Exons
(0, 0)
Info
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.
(no "Exon" information available for biological units yet)
SCOP Domains
(3, 3)
Info
All SCOP Domains
1a: SCOP_d3bi0a1 (A:594-750)
2a: SCOP_d3bi0a3 (A:57-117,A:351-593)
3a: SCOP_d3bi0a2 (A:118-350)
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(
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(
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
N-cbl like
(37)
Superfamily
:
Transferrin receptor-like dimerisation domain
(18)
Family
:
Transferrin receptor-like dimerisation domain
(18)
Protein domain
:
Glutamate carboxypeptidase II
(14)
Human (Homo sapiens) [TaxId: 9606]
(14)
1a
d3bi0a1
A:594-750
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Phosphorylase/hydrolase-like
(558)
Superfamily
:
Zn-dependent exopeptidases
(214)
Family
:
FolH catalytic domain-like
(18)
Protein domain
:
Glutamate carboxypeptidase II FOLH1
(14)
Human (Homo sapiens) [TaxId: 9606]
(14)
2a
d3bi0a3
A:57-117,A:351-593
Fold
:
The swivelling beta/beta/alpha domain
(136)
Superfamily
:
PA domain
(18)
Family
:
PA domain
(18)
Protein domain
:
Glutamate carboxypeptidase II
(14)
Human (Homo sapiens) [TaxId: 9606]
(14)
3a
d3bi0a2
A:118-350
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]
CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Protein & NOT Site
Protein & NOT PROSITE
Chain A
Asymmetric Unit 1
Asymmetric Unit 2
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