SMTL ID : 2bc4.3 (2 other biounits)

Crystal structure of HLA-DM

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.27 Å

Oligo State

hetero-2-2-mer

Ligands

2 x NAG- NDG- BMA- BMA: beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NDG-BMA-BMA.1: 9 residues within 4Å: Chain A: L.13, N.15 Chain B: L.12, K.20 Chain D: F.48, G.49, V.50, N.52, S.53 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:N.15, D:F.48, D:F.48 Water bridges: A:L.13, A:N.15, D:V.50 NAG-NDG-BMA-BMA.4: 10 residues within 4Å: Chain B: F.48, G.49, V.50, N.52, S.53 Chain C: D.12, L.13, N.15 Chain D: L.12, K.20 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain C Water bridges: B:V.50, C:D.12, C:N.15 Hydrogen bonds: C:N.15, B:F.48, B:F.48, B:N.52

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.3: 2 residues within 4Å: Chain B: H.145 Chain C: R.184 Ligand excluded by PLIP CL.5: 1 residues within 4Å: Chain C: D.68 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: R.98, R.184 Chain D: H.145 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nicholson, M.J. et al., Small molecules that enhance the catalytic efficiency of HLA-DM. J.Immunol. (2006)

Release Date

2006-05-23

Peptides

HLA class II histocompatibility antigen, DM alpha chain: AC
HLA class II histocompatibility antigen, DM beta chain: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

HLA class II histocompatibility antigen, DM alpha chain

HLA class II histocompatibility antigen, DM beta chain

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