1MCD

PRINCIPLES AND PITFALLS IN DESIGNING SITE DIRECTED PEPTIDE LIGANDS

Structural Biology Knowledgebase: 1MCD SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Observed: 0.190

Literature

Macromolecules
Sequence Display for 1MCD

Classification: IMMUNOGLOBULIN

Total Structure Weight: 46630.65

Macromolecule Entities
Molecule Chains Length Organism Details
IMMUNOGLOBULIN LAMBDA DIMER MCG (LIGHT CHAIN) A, B 216 Homo sapiens Mutation: F20I, S23T, I29V, N31G, R39Q, P42A, L48V, M49I, T54N, N62D, A94E, N97D, S98N, L99F, I100V, G103T, R106K, L107V, A116N, S118T, S156G, T167K
PEPTIDE N-ACETYL-D-PHE-B-ALA-L-HIS-D-PRO-NH2 P 6 synthetic

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
DPN
Query on DPN

P D-PHENYLALANINE
C9 H11 N O2
COLNVLDHVKWLRT-MRVPVSSYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
HIS
Query on HIS

P HISTIDINE
C6 H10 N3 O2
HNDVDQJCIGZPNO-YFKPBYRVSA-O
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DPR
Query on DPR

P D-PROLINE
C5 H9 N O2
ONIBWKKTOPOVIA-SCSAIBSYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACE
Query on ACE

A, P ACETYL GROUP
C2 H4 O
IKHGUXGNUITLKF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NH2
Query on NH2

A, P AMINO GROUP
H2 N
QGZKDVFQNNGYKY-UHFFFAOYAF
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 3 Unique
ID Chains Type Formula 2D Diagram Parent
ACE
Query on ACE
A, P NON-POLYMER C2 H4 O --
BAL
Query on BAL
P peptide-like C3 H7 N O2 --
NH2
Query on NH2
A, P NON-POLYMER H2 N --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Observed: 0.190
  • Space Group: P 31 2 1

Unit Cell:

Length (Å) Angle (°)
a = 72.30 α = 90.00
b = 72.30 β = 90.00
c = 185.90 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1993-02-25
  • Released Date: 1994-01-31
  • Deposition author(s): Edmundson, A.B., Harris, D.L., Fan, Z.-C., Guddat, L.W.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update