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5L9Z
Asym. Unit
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Asym.Unit (94 KB)
Biol.Unit 1 (88 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN HEPARANASE NUCLEOPHILE MUTANT (E343Q), IN COMPLEX WITH UNREACTED GLUCURONIC ACID CONFIGURED AZIRIDINE PROBE JJB355
Authors
:
L. Wu, Y. Jin, G. J. Davies
Date
:
13 Jun 16 (Deposition) - 31 May 17 (Release) - 14 Jun 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.57
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Heparanase, Probe, Gh79, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. Wu, J. Jiang, Y. Jin, W. W. Kallemeijn, C. L. Kuo, M. Artola, W. Dai, C. Van Elk, M. Van Eijk, G. A. Van Der Marel, J. D. C. Codee, B. I. Florea, J. M. F. G. Aerts, H. S. Overkleeft, G. J. Davies
Activity-Based Probes For Functional Interrogation Of Retaining Beta-Glucuronidases.
Nat. Chem. Biol. 2017
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Hetero Components
(4, 15)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
2f: 1,2-ETHANEDIOL (EDOf)
2g: 1,2-ETHANEDIOL (EDOg)
3a: (1~{R},2~{S},3~{R},4~{S},5~{S},6~{... (GUXa)
4a: N-ACETYL-D-GLUCOSAMINE (NAGa)
4b: N-ACETYL-D-GLUCOSAMINE (NAGb)
4c: N-ACETYL-D-GLUCOSAMINE (NAGc)
4d: N-ACETYL-D-GLUCOSAMINE (NAGd)
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No.
Name
Count
Type
Full Name
1
CL
3
Ligand/Ion
CHLORIDE ION
2
EDO
7
Ligand/Ion
1,2-ETHANEDIOL
3
GUX
1
Ligand/Ion
(1~{R},2~{S},3~{R},4~{S},5~{S},6~{R})-7-[8-[(AZANYLIDENE-{4}-AZANYLIDENE)AMINO]OCTYL]-3,4,5-TRIS(OXIDANYL)-7-AZABICYCLO[4.1.0]HEPTANE-2-CARBOXYLICACID
4
NAG
4
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
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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: AD1 (SOFTWARE)
11: AD2 (SOFTWARE)
12: AD3 (SOFTWARE)
13: AD4 (SOFTWARE)
14: AD5 (SOFTWARE)
15: AD6 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY A:415 , THR A:416 , ASN A:439 , THR A:440 , HOH A:730 , HOH A:922
binding site for residue EDO A 605
02
AC2
SOFTWARE
PHE A:327 , MET A:375 , HOH A:889 , HOH A:935 , HOH A:950 , HIS B:50
binding site for residue EDO A 606
03
AC3
SOFTWARE
ARG A:307 , HIS A:486 , LEU A:488 , LEU A:489 , HOH A:741
binding site for residue EDO A 607
04
AC4
SOFTWARE
GLN A:324 , HOH A:715 , HOH A:722 , HOH A:784 , HOH A:954
binding site for residue EDO A 608
05
AC5
SOFTWARE
LYS A:477 , ASN A:496 , LYS A:514 , HOH A:723
binding site for residue EDO A 609
06
AC6
SOFTWARE
PRO A:353 , HOH A:882
binding site for residue EDO A 610
07
AC7
SOFTWARE
LYS A:337 , HOH A:989
binding site for residue CL A 611
08
AC8
SOFTWARE
GLY A:239 , MET A:278 , HOH A:726 , HOH A:896
binding site for residue CL A 612
09
AC9
SOFTWARE
ALA A:388 , HOH B:346 , HOH B:360
binding site for residue CL A 613
10
AD1
SOFTWARE
ASN A:224 , GLU A:225 , GLN A:270 , TYR A:298 , GLN A:343 , TYR A:348 , GLY A:349 , GLY A:350 , GLN A:383 , TYR A:391 , HOH A:708 , HOH A:908 , ASP B:62 , GLY B:96 , THR B:97 , HOH B:304
binding site for residue GUX A 614
11
AD2
SOFTWARE
CYS A:179 , PRO B:78 , ARG B:81 , ARG B:85 , HOH B:301
binding site for residue EDO B 201
12
AD3
SOFTWARE
ASN A:200 , SER A:202 , HOH A:812 , HOH A:894 , HOH A:937
binding site for Mono-Saccharide NAG A 601 bound to ASN A 200
13
AD4
SOFTWARE
ASN A:217
binding site for Mono-Saccharide NAG A 604 bound to ASN A 217
14
AD5
SOFTWARE
ASN A:238 , GLN A:241 , HOH A:703 , HOH A:710 , HOH A:718 , HOH A:795 , HOH A:825
binding site for Mono-Saccharide NAG A 602 bound to ASN A 238
15
AD6
SOFTWARE
ASN A:459 , HOH A:756 , HOH A:803 , HOH A:834 , HOH A:932 , HOH A:956
binding site for Mono-Saccharide NAG A 603 bound to ASN A 459
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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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Asymmetric Unit 1
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Asym.Unit (94 KB)
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