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4OC2
Biol. Unit 1
Info
Asym.Unit (279 KB)
Biol.Unit 1 (539 KB)
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(1)
Title
:
X-RAY STRUCTURE OF OF HUMAN GLUTAMATE CARBOXYPEPTIDASE II (GCPII) IN A COMPLEX WITH CEIBZL, A UREA-BASED INHIBITOR N~2~-{[(1S)-1-CARBOXYBUT-3-YN-1-YL]CARBAMOYL}-N~6~-(4-IODOBENZOYL)-L-LYSINE
Authors
:
J. Pavlicek, J. Ptacek, J. Cerny, Y. Byun, L. Skultetyova, M. Pomper, J. Lubkowski, C. Barinka
Date
:
08 Jan 14 (Deposition) - 21 May 14 (Release) - 21 May 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.65
Chains
:
Asym. Unit : A
Biol. Unit 1: A (2x)
Keywords
:
Hydrolase, Metallopeptidase, Hydrolase-Hydrolase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Pavlicek, J. Ptacek, J. Cerny, Y. Byun, L. Skultetyova, M. G. Pomper J. Lubkowski, C. Barinka
Structural Characterization Of P1'-Diversified Urea-Based Inhibitors Of Glutamate Carboxypeptidase Ii.
Bioorg. Med. Chem. Lett. V. 24 2340 2014
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Hetero Components
(5, 34)
Info
All Hetero Components
1a: N~2~-{[(1S)-1-CARBOXYBUT-3-YN-1-YL... (2QQa)
2a: BETA-D-MANNOSE (BMAa)
2b: BETA-D-MANNOSE (BMAb)
3a: CALCIUM ION (CAa)
4a: CHLORIDE ION (CLa)
5a: ALPHA-L-FUCOSE (FUCa)
5b: ALPHA-L-FUCOSE (FUCb)
6a: ALPHA-D-MANNOSE (MANa)
7a: N-ACETYL-D-GLUCOSAMINE (NAGa)
7b: N-ACETYL-D-GLUCOSAMINE (NAGb)
7c: N-ACETYL-D-GLUCOSAMINE (NAGc)
7d: N-ACETYL-D-GLUCOSAMINE (NAGd)
7e: N-ACETYL-D-GLUCOSAMINE (NAGe)
7f: N-ACETYL-D-GLUCOSAMINE (NAGf)
7g: N-ACETYL-D-GLUCOSAMINE (NAGg)
7h: N-ACETYL-D-GLUCOSAMINE (NAGh)
7i: N-ACETYL-D-GLUCOSAMINE (NAGi)
7j: N-ACETYL-D-GLUCOSAMINE (NAGj)
7k: N-ACETYL-D-GLUCOSAMINE (NAGk)
8a: ZINC ION (ZNa)
8b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
2QQ
2
Ligand/Ion
N~2~-{[(1S)-1-CARBOXYBUT-3-YN-1-YL]CARBAMOYL}-N~6~-(4-IODOBENZOYL)-L-LYSINE
2
BMA
4
Ligand/Ion
BETA-D-MANNOSE
3
CA
-1
Ligand/Ion
CALCIUM ION
4
CL
-1
Ligand/Ion
CHLORIDE ION
5
FUC
4
Ligand/Ion
ALPHA-L-FUCOSE
6
MAN
2
Ligand/Ion
ALPHA-D-MANNOSE
7
NAG
22
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
8
ZN
-1
Ligand/Ion
ZINC ION
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Sites
(21, 21)
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)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:76 , GLN A:99 , NAG A:802 , HOH A:1131 , HOH A:1158 , HOH A:1351
BINDING SITE FOR RESIDUE NAG A 801
02
AC2
SOFTWARE
NAG A:801 , HOH A:1138
BINDING SITE FOR RESIDUE NAG A 802
03
AC3
SOFTWARE
ASN A:121 , THR A:123 , HIS A:124 , THR A:349 , FUC A:804
BINDING SITE FOR RESIDUE NAG A 803
04
AC4
SOFTWARE
THR A:123 , HIS A:124 , NAG A:803
BINDING SITE FOR RESIDUE FUC A 804
05
AC5
SOFTWARE
TYR A:127 , GLU A:137 , ILE A:138 , ASN A:140 , NAG A:806 , FUC A:807
BINDING SITE FOR RESIDUE NAG A 805
06
AC6
SOFTWARE
NAG A:805 , HOH A:1221
BINDING SITE FOR RESIDUE NAG A 806
07
AC7
SOFTWARE
NAG A:805
BINDING SITE FOR RESIDUE FUC A 807
08
AC8
SOFTWARE
ASN A:195 , SER A:197
BINDING SITE FOR RESIDUE NAG A 808
09
AC9
SOFTWARE
TRP A:246 , ASN A:459 , PHE A:565 , TYR A:566 , HOH A:976 , HOH A:1149 , HOH A:1397 , HOH A:1411
BINDING SITE FOR RESIDUE NAG A 809
10
BC1
SOFTWARE
SER A:472 , ASN A:476 , PRO A:594 , NAG A:811 , HOH A:1326 , HOH A:1394
BINDING SITE FOR RESIDUE NAG A 810
11
BC2
SOFTWARE
GLN A:651 , NAG A:810 , BMA A:812 , HOH A:1395 , HOH A:1406 , HOH A:1407
BINDING SITE FOR RESIDUE NAG A 811
12
BC3
SOFTWARE
GLN A:651 , NAG A:811
BINDING SITE FOR RESIDUE BMA A 812
13
BC4
SOFTWARE
SER A:631 , SER A:634 , ASN A:638 , GLN A:740 , NAG A:814 , HOH A:1024 , HOH A:1056 , HOH A:1206
BINDING SITE FOR RESIDUE NAG A 813
14
BC5
SOFTWARE
NAG A:813 , BMA A:815
BINDING SITE FOR RESIDUE NAG A 814
15
BC6
SOFTWARE
HIS A:112 , GLU A:276 , LYS A:324 , ARG A:354 , NAG A:814 , MAN A:816
BINDING SITE FOR RESIDUE BMA A 815
16
BC7
SOFTWARE
PHE A:235 , LYS A:240 , SER A:241 , GLU A:276 , BMA A:815 , HOH A:1083 , HOH A:1204 , HOH A:1207 , HOH A:1283
BINDING SITE FOR RESIDUE MAN A 816
17
BC8
SOFTWARE
ASP A:387 , GLU A:425 , HIS A:553 , ZN A:818 , 2QQ A:821 , HOH A:1348
BINDING SITE FOR RESIDUE ZN A 817
18
BC9
SOFTWARE
HIS A:377 , ASP A:387 , GLU A:424 , GLU A:425 , ASP A:453 , ZN A:817 , HOH A:1348
BINDING SITE FOR RESIDUE ZN A 818
19
CC1
SOFTWARE
THR A:269 , TYR A:272 , GLU A:433 , GLU A:436 , HOH A:905
BINDING SITE FOR RESIDUE CA A 819
20
CC2
SOFTWARE
ASN A:451 , ASP A:453 , ARG A:534 , ARG A:536
BINDING SITE FOR RESIDUE CL A 820
21
CC3
SOFTWARE
ARG A:210 , ASN A:257 , GLU A:424 , GLU A:425 , ARG A:463 , ASP A:465 , GLY A:518 , ASN A:519 , ARG A:534 , ARG A:536 , PHE A:546 , TYR A:552 , HIS A:553 , TYR A:700 , ZN A:817 , HOH A:908 , HOH A:1065 , HOH A:1348 , HOH A:1349
BINDING SITE FOR RESIDUE 2QQ A 821
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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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.
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SCOP Domains
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CATH Domains
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Pfam Domains
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Sorry, no Info available
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Atom Selection
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Protein & NOT Variant
Protein & NOT Site
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Chain A
Asymmetric Unit 1
Asymmetric Unit 2
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select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
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Asym.Unit (279 KB)
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Header - Biol.Unit 1
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