1H8L

DUCK CARBOXYPEPTIDASE D DOMAIN II IN COMPLEX WITH GEMSA

Structural Biology Knowledgebase: 1H8L SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.239
  • R-Value Work: 0.199

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1H8L

Classification: CARBOXYPEPTIDASE

Total Structure Weight: 44966.61

Macromolecule Entities
Molecule Chains Length Organism Details
CARBOXYPEPTIDASE GP180 RESIDUES 503-882 A 380 Lophonetta specularioides EC#: 3.4.17.22 IUBMB
Fragment: YES
Gene Name(s): CPD Gene View

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
GEM
Query on GEM

A (2-GUANIDINOETHYLMERCAPTO)SUCCINIC ACID
2-GUANIDINOETHYLTHIO)SUCCINIC ACID; GUANIDINOETHYL MERCAPTOSUCCINIC ACID; GEMSA (Synonym)
C7 H13 N3 O4 S
VKVCLXDFOQQABP-BYPYZUCNSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NDG
Query on NDG

A 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

A N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BMA
Query on BMA

A BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
GEM N/A in BindingDB
N/A in BindingMoad
Ki: 34 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.239
  • R-Value Work: 0.199
  • Space Group: P 21 3

Unit Cell:

Length (Å) Angle (°)
a = 136.48 α = 90.00
b = 136.48 β = 90.00
c = 136.48 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-02-09
  • Released Date: 2002-02-08
  • Deposition author(s): Gomis-Rueth, F.X., Coll, M., Aviles, F.X., Vendrell, J., Fricker, L.D.

Revision History

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