1HV5

CRYSTAL STRUCTURE OF THE STROMELYSIN-3 (MMP-11) CATALYTIC DOMAIN COMPLEXED WITH A PHOSPHINIC INHIBITOR

Structural Biology Knowledgebase: 1HV5 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.262
  • R-Value Work: 0.218

Literature

Macromolecules
Sequence Display for 1HV5

Classification: hydrolase

Total Structure Weight: 126977.54

Macromolecule Entities
Molecule Chains Length Organism Details
STROMELYSIN 3 A, B, C..., D, E, FA, B, C, D, E, F 165 Mus musculus EC#: 3.4.24 IUBMB
Gene Name(s): Mmp11
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
RXP
Query on RXP

A, B, C, D, E, F 1-BENZYLOXYCARBONYLAMINO-2-PHENYL-ETHYL)- {2-[1-CARBAMOYL-2-(1H-INDOL-3-YL)-ETHYLCARBAMOYL]- 5-PHENYL-PENTYL}-PHOSPHINIC ACID
C39 H43 N4 O6 P
YQEMFOGNUTYMTJ-JNBVYXHXSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CPS
Query on CPS

A, B, C, D, E, F 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1- PROPANESULFONATE
CHAPS (Synonym)
C32 H58 N2 O7 S
UMCMPZBLKLEWAF-BCTGSCMUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B, C, D, E, F ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A, B, C, D, E, F CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
RXP N/A in BindingDB
N/A in BindingMoad
Ki: 5 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.262
  • R-Value Work: 0.218
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 140.10 α = 90.00
b = 148.50 β = 90.00
c = 91.40 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-01-08
  • Released Date: 2001-03-28
  • Deposition author(s): Gall, A.L., Ruff, M., Kannan, R., Cuniasse, P., Yiotakis, A., Dive, V., Rio, M.C., Basset, P., Moras, D.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4