SMTL ID : 3rg1.1 (3 other biounits)

Crystal structure of the RP105/MD-1 complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.91 Å

Oligo State

hetero-2-2-mer

Ligands

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

NAG-NAG-BMA.1: 8 residues within 4Å: Chain A: Y.384, L.403, D.405, A.407, N.430, H.452 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.2, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.2 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 10 residues within 4Å: Chain B: Y.384, L.403, D.405, A.407, V.428, N.430, H.452 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.4, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.4, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.4 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.2: 20 residues within 4Å: Chain A: K.332, G.333, S.357, H.358, Y.379, N.381, S.383, Y.384, D.405 Chain C: F.60, D.62, S.76, P.78, E.81, Y.123, Q.125, D.126, H.127 Ligands: NAG-NAG-BMA.1, NAG-NAG-BMA.1 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.125, C:H.127, C:D.126 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.4: 22 residues within 4Å: Chain B: K.332, G.333, S.357, H.358, Y.379, N.381, S.383, Y.384, L.403, D.405 Chain D: F.60, D.62, S.76, P.78, E.81, Y.123, Q.125, D.126, H.127 Ligands: NAG-NAG-BMA.3, NAG-NAG-BMA.3, NAG-NAG-BMA.3 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.125, D:D.126, D:D.126

1 x PGT: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE(Non-covalent)

PGT.5: 11 residues within 4Å: Chain D: F.48, F.75, Y.77, V.79, F.89, I.98, I.104, N.106, P.107, F.109, L.122 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:F.48, D:F.48, D:Y.77, D:V.79, D:F.89, D:F.89, D:I.98, D:I.104, D:I.104, D:N.106, D:F.109

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yoon, S.I. et al., An unusual dimeric structure and assembly for TLR4 regulator RP105-MD-1. Nat.Struct.Mol.Biol. (2011)

Release Date

2011-08-31

Peptides

CD180 molecule: AB
LY86 protein: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

CD180 molecule

LY86 protein

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