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5LA7
Biol. Unit 1
Info
Asym.Unit (96 KB)
Biol.Unit 1 (90 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN PROHEPARANASE, IN COMPLEX WITH 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
:
1.94
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Hydrolase, Heparanase, Proenzyme, Gh79
(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, 13)
Info
All Hetero Components
1a: (1~{S},2~{R},3~{S},4~{S},5~{S},6~{... (6S6a)
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)
3a: ALPHA-L-FUCOSE (FUCa)
4a: N-ACETYL-D-GLUCOSAMINE (NAGa)
4b: N-ACETYL-D-GLUCOSAMINE (NAGb)
4c: N-ACETYL-D-GLUCOSAMINE (NAGc)
4d: N-ACETYL-D-GLUCOSAMINE (NAGd)
4e: N-ACETYL-D-GLUCOSAMINE (NAGe)
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No.
Name
Count
Type
Full Name
1
6S6
1
Ligand/Ion
(1~{S},2~{R},3~{S},4~{S},5~{S},6~{R})-2-(8-AZIDOOCTYLAMINO)-3,4,5,6-TETRAKIS(OXIDANYL)CYCLOHEXANE-1-CARBOXYLIC ACID
2
EDO
6
Ligand/Ion
1,2-ETHANEDIOL
3
FUC
1
Ligand/Ion
ALPHA-L-FUCOSE
4
NAG
5
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
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Sites
(11, 11)
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)
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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PHE A:410 , VAL A:414 , GLY A:415 , THR A:416 , EDO A:608 , HOH A:731
binding site for residue EDO A 607
02
AC2
SOFTWARE
PRO A:54 , LYS A:411 , VAL A:414 , ASN A:439 , EDO A:607 , HOH A:716
binding site for residue EDO A 608
03
AC3
SOFTWARE
PRO A:509 , PRO A:510 , LEU A:511 , MET A:512 , HOH A:717
binding site for residue EDO A 609
04
AC4
SOFTWARE
TYR A:174 , ASN A:178 , LEU A:182 , ASP A:183 , LEU A:184 , ASN A:217
binding site for residue EDO A 610
05
AC5
SOFTWARE
PHE A:327 , GLU A:331 , PRO A:335 , GLY A:336 , LYS A:337
binding site for residue EDO A 611
06
AC6
SOFTWARE
ASP A:68 , GLN A:147 , ARG A:428
binding site for residue EDO A 612
07
AC7
SOFTWARE
ASP A:62 , GLY A:96 , THR A:97 , HIS A:155 , ASN A:224 , GLU A:225 , TYR A:298 , GLU A:343 , TYR A:348 , GLY A:349 , GLY A:350 , GLN A:383 , TYR A:391 , HOH A:785
binding site for residue 6S6 A 613
08
AC8
SOFTWARE
PHE A:160 , ASN A:162 , LEU A:192
binding site for Mono-Saccharide NAG A 601 bound to ASN A 162
09
AC9
SOFTWARE
ASN A:200 , SER A:202
binding site for Mono-Saccharide NAG A 602 bound to ASN A 200
10
AD1
SOFTWARE
ASN A:238 , GLN A:241 , ARG A:254
binding site for Mono-Saccharide NAG A 603 bound to ASN A 238
11
AD2
SOFTWARE
VAL A:122 , ASN A:123 , LYS A:430 , HIS A:458 , ASN A:459 , LYS A:462 , HOH A:750 , HOH A:772
binding site for Poly-Saccharide residues NAG A 604 through FUC A 606 bound to ASN A 459
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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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Pfam Domains
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Chain A
Asymmetric Unit 1
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Asym.Unit (96 KB)
Header - Asym.Unit
Biol.Unit 1 (90 KB)
Header - Biol.Unit 1
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