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2OR4
Asym. Unit
Info
Asym.Unit (146 KB)
Biol.Unit 1 (273 KB)
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(1)
Title
:
A HIGH RESOLUTION CRYSTAL STRUCTURE OF HUMAN GLUTAMATE CARBOXYPEPTIDASE II IN COMPLEX WITH QUISQUALIC ACID
Authors
:
C. Barinka, J. Lubkowski
Date
:
01 Feb 07 (Deposition) - 12 Jun 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.62
Chains
:
Asym. Unit : A
Biol. Unit 1: A (2x)
Keywords
:
Prostate Specific Membrane Antigen, Metallopeptidase, Folate Hydrolase, Glutamate Carboxypeptidase Ii, Naaladase, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. Barinka, M. Rovenska, P. Mlcochova, K. Hlouchova, A. Plechanovova P. Majer, T. Tsukamoto, B. S. Slusher, J. Konvalinka, J. Lubkowski
Structural Insight Into The Pharmacophore Pocket Of Human Glutamate Carboxypeptidase Ii.
J. Med. Chem. V. 50 3267 2007
[
close entry info
]
Hetero Components
(7, 18)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
2a: CALCIUM ION (CAa)
3a: CHLORIDE ION (CLa)
4a: ALPHA-D-MANNOSE (MANa)
5a: N-ACETYL-D-GLUCOSAMINE (NAGa)
5b: N-ACETYL-D-GLUCOSAMINE (NAGb)
5c: N-ACETYL-D-GLUCOSAMINE (NAGc)
5d: N-ACETYL-D-GLUCOSAMINE (NAGd)
5e: N-ACETYL-D-GLUCOSAMINE (NAGe)
5f: N-ACETYL-D-GLUCOSAMINE (NAGf)
5g: N-ACETYL-D-GLUCOSAMINE (NAGg)
5h: N-ACETYL-D-GLUCOSAMINE (NAGh)
5i: N-ACETYL-D-GLUCOSAMINE (NAGi)
5j: N-ACETYL-D-GLUCOSAMINE (NAGj)
5k: N-ACETYL-D-GLUCOSAMINE (NAGk)
6a: (S)-2-AMINO-3-(3,5-DIOXO-[1,2,4]OX... (QUSa)
7a: ZINC ION (ZNa)
7b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
1
Ligand/Ion
BETA-D-MANNOSE
2
CA
1
Ligand/Ion
CALCIUM ION
3
CL
1
Ligand/Ion
CHLORIDE ION
4
MAN
1
Ligand/Ion
ALPHA-D-MANNOSE
5
NAG
11
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
6
QUS
1
Ligand/Ion
(S)-2-AMINO-3-(3,5-DIOXO-[1,2,4]OXADIAZOLIDIN-2-YL)-PROPIONIC ACID
7
ZN
2
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
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:2042 , HOH A:2076 , HOH A:2579 , HOH A:2644
BINDING SITE FOR RESIDUE NAG A 1755
02
AC2
SOFTWARE
NAG A:1755 , HOH A:2051 , HOH A:2416 , HOH A:2574 , HOH A:2647
BINDING SITE FOR RESIDUE NAG A 1756
03
AC3
SOFTWARE
ASN A:121 , THR A:123 , HIS A:124 , HOH A:2402 , HOH A:2558 , HOH A:2564
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:2247 , HOH A:2520 , HOH A:2552 , HOH A:2560
BINDING SITE FOR RESIDUE NAG A 1758
05
AC5
SOFTWARE
NAG A:1758 , HOH A:2171 , HOH A:2285 , HOH A:2398
BINDING SITE FOR RESIDUE NAG A 1767
06
AC6
SOFTWARE
ASN A:195 , SER A:197 , HOH A:2572 , HOH A:2583
BINDING SITE FOR RESIDUE NAG A 1759
07
AC7
SOFTWARE
TRP A:246 , ASN A:459 , PHE A:565 , TYR A:566 , HOH A:1877 , HOH A:2066 , HOH A:2317 , HOH A:2360 , HOH A:2426
BINDING SITE FOR RESIDUE NAG A 1760
08
AC8
SOFTWARE
SER A:472 , ASN A:476 , PRO A:594 , NAG A:1762 , HOH A:2328 , HOH A:2346 , HOH A:2394 , HOH A:2657
BINDING SITE FOR RESIDUE NAG A 1761
09
AC9
SOFTWARE
GLN A:651 , NAG A:1761 , HOH A:2276 , HOH A:2315 , HOH A:2324 , HOH A:2382 , HOH A:2546 , HOH A:2559
BINDING SITE FOR RESIDUE NAG A 1762
10
BC1
SOFTWARE
SER A:631 , SER A:634 , ASN A:638 , GLN A:740 , NAG A:1764 , HOH A:1926 , HOH A:1960 , HOH A:2141 , HOH A:2361 , HOH A:2570
BINDING SITE FOR RESIDUE NAG A 1763
11
BC2
SOFTWARE
GLU A:276 , NAG A:1763 , BMA A:1765 , HOH A:2361
BINDING SITE FOR RESIDUE NAG A 1764
12
BC3
SOFTWARE
HIS A:112 , GLU A:276 , LYS A:324 , ARG A:354 , NAG A:1764 , MAN A:1766 , HOH A:2329 , HOH A:2356
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:1990 , HOH A:2139 , HOH A:2142 , HOH A:2300 , HOH A:2478
BINDING SITE FOR RESIDUE MAN A 1766
14
BC5
SOFTWARE
ASP A:387 , GLU A:425 , HIS A:553 , ZN A:1752 , HOH A:2675
BINDING SITE FOR RESIDUE ZN A 1751
15
BC6
SOFTWARE
HIS A:377 , ASP A:387 , GLU A:424 , ASP A:453 , ZN A:1751 , HOH A:2675
BINDING SITE FOR RESIDUE ZN A 1752
16
BC7
SOFTWARE
THR A:269 , TYR A:272 , GLU A:433 , GLU A:436 , HOH A:1806
BINDING SITE FOR RESIDUE CA A 1753
17
BC8
SOFTWARE
ASN A:451 , ASP A:453 , ARG A:534 , ARG A:536
BINDING SITE FOR RESIDUE CL A 1754
18
BC9
SOFTWARE
ARG A:210 , ASN A:257 , GLU A:424 , GLY A:427 , LEU A:428 , SER A:517 , GLY A:518 , ASN A:519 , TYR A:552 , HIS A:553 , LYS A:699 , TYR A:700 , HOH A:1809 , HOH A:1974 , HOH A:2296
BINDING SITE FOR RESIDUE QUS A 1801
[
close Site info
]
SAPs(SNPs)/Variants
(3, 3)
Info
(mutated residues are not available)
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)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
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]
Exons
(18, 18)
Info
All Exons
Exon 1.5 (A:55-75)
Exon 1.6c (A:75-137)
Exon 1.7a (A:138-171 (gaps))
Exon 1.8a (A:172-213)
Exon 1.9b (A:214-276)
Exon 1.10 (A:276-307)
Exon 1.11b (A:307-340)
Exon 1.12a (A:340-369)
Exon 1.13 (A:369-409)
Exon 1.14 (A:409-436)
Exon 1.15 (A:437-458)
Exon 1.16 (A:458-480)
Exon 1.18 (A:481-511)
Exon 1.19a (A:511-540)
Exon 1.20a (A:544-630)
Exon 1.21b (A:630-657)
Exon 1.22 (A:657-688)
Exon 1.23d (A:688-750)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.1a/1.5
02: Boundary 1.5/1.6c
03: Boundary 1.6c/1.7a
04: Boundary 1.7a/1.8a
05: Boundary 1.8a/1.9b
06: Boundary 1.9b/1.10
07: Boundary 1.10/1.11b
08: Boundary 1.11b/1.12a
09: Boundary 1.12a/1.13
10: Boundary 1.13/1.14
11: Boundary 1.14/1.15
12: Boundary 1.15/1.16
13: Boundary 1.16/1.18
14: Boundary 1.18/1.19a
15: Boundary 1.19a/1.20a
16: Boundary 1.20a/1.21b
17: Boundary 1.21b/1.22
18: Boundary 1.22/1.23d
19: Boundary 1.23d/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1a
ENST00000256999
1a
ENSE00001364015
chr11:
49230222-49229844
379
FOLH1_HUMAN
1-40
40
0
-
-
1.5
ENST00000256999
5
ENSE00001771797
chr11:
49227724-49227619
106
FOLH1_HUMAN
40-75
36
1
A:55-75
21
1.6c
ENST00000256999
6c
ENSE00001804269
chr11:
49221993-49221807
187
FOLH1_HUMAN
75-137
63
1
A:75-137
63
1.7a
ENST00000256999
7a
ENSE00001603272
chr11:
49214446-49214345
102
FOLH1_HUMAN
138-171
34
1
A:138-171 (gaps)
34
1.8a
ENST00000256999
8a
ENSE00001701397
chr11:
49208321-49208196
126
FOLH1_HUMAN
172-213
42
1
A:172-213
42
1.9b
ENST00000256999
9b
ENSE00001627795
chr11:
49207407-49207221
187
FOLH1_HUMAN
214-276
63
1
A:214-276
63
1.10
ENST00000256999
10
ENSE00001652660
chr11:
49204794-49204701
94
FOLH1_HUMAN
276-307
32
1
A:276-307
32
1.11b
ENST00000256999
11b
ENSE00001780619
chr11:
49197509-49197411
99
FOLH1_HUMAN
307-340
34
1
A:307-340
34
1.12a
ENST00000256999
12a
ENSE00001612233
chr11:
49196529-49196444
86
FOLH1_HUMAN
340-369
30
1
A:340-369
30
1.13
ENST00000256999
13
ENSE00001643735
chr11:
49195028-49194909
120
FOLH1_HUMAN
369-409
41
1
A:369-409
41
1.14
ENST00000256999
14
ENSE00001765179
chr11:
49192829-49192747
83
FOLH1_HUMAN
409-436
28
1
A:409-436
28
1.15
ENST00000256999
15
ENSE00001800342
chr11:
49190810-49190747
64
FOLH1_HUMAN
437-458
22
1
A:437-458
22
1.16
ENST00000256999
16
ENSE00001739662
chr11:
49186324-49186257
68
FOLH1_HUMAN
458-480
23
1
A:458-480
23
1.18
ENST00000256999
18
ENSE00001704015
chr11:
49179595-49179504
92
FOLH1_HUMAN
481-511
31
1
A:481-511
31
1.19a
ENST00000256999
19a
ENSE00001639568
chr11:
49178359-49178269
91
FOLH1_HUMAN
511-541
31
1
A:511-540
30
1.20a
ENST00000256999
20a
ENSE00001804599
chr11:
49176044-49175780
265
FOLH1_HUMAN
542-630
89
1
A:544-630
87
1.21b
ENST00000256999
21b
ENSE00001637755
chr11:
49175479-49175398
82
FOLH1_HUMAN
630-657
28
1
A:630-657
28
1.22
ENST00000256999
22
ENSE00001748529
chr11:
49170283-49170191
93
FOLH1_HUMAN
657-688
32
1
A:657-688
32
1.23d
ENST00000256999
23d
ENSE00002199992
chr11:
49168497-49168187
311
FOLH1_HUMAN
688-750
63
1
A:688-750
63
[
close EXON info
]
SCOP Domains
(3, 3)
Info
All SCOP Domains
1a: SCOP_d2or4a1 (A:594-750)
2a: SCOP_d2or4a3 (A:57-117,A:351-593)
3a: SCOP_d2or4a2 (A:118-350)
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Protein Domains
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Organisms
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)
(
)
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
d2or4a1
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
d2or4a3
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
d2or4a2
A:118-350
[
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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Sorry, no Info available
[
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Pfam Domains
(3, 3)
Info
all PFAM domains
1a: PFAM_Peptidase_M28_2or4A01 (A:370-560)
2a: PFAM_PA_2or4A02 (A:165-263)
3a: PFAM_TFR_dimer_2or4A03 (A:626-749)
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Clan
:
Peptidase_MH
(119)
Family
:
Peptidase_M28
(38)
Homo sapiens (Human)
(30)
1a
Peptidase_M28-2or4A01
A:370-560
Clan
:
no clan defined [family: PA]
(15)
Family
:
PA
(15)
Homo sapiens (Human)
(12)
2a
PA-2or4A02
A:165-263
Clan
:
no clan defined [family: TFR_dimer]
(12)
Family
:
TFR_dimer
(12)
Homo sapiens (Human)
(12)
3a
TFR_dimer-2or4A03
A:626-749
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