SMTL ID : 3t6q.1

Crystal structure of mouse RP105/MD-1 complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-2-2-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]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(Non-covalent)

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.1: 23 residues within 4Å: Chain A: K.333, G.334, S.358, H.359, N.382, S.384, Y.385, L.404, D.406 Chain B: F.63, D.65, S.79, Y.80, P.81, E.84, Y.126, E.128, N.129, R.130 Ligands: NAG-NAG.2, NAG-NAG.2, GOL.8, GOL.11 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.128, B:N.129 Water bridges: B:R.130

3 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 9 residues within 4Å: Chain A: Y.385, L.404, D.406, A.408, V.429, N.431, H.453 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.1, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.1 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.429 NAG-NAG.3: 4 residues within 4Å: Chain C: N.50, T.51, S.54, Q.78 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 9 residues within 4Å: Chain C: Y.385, L.404, D.406, A.408, V.429, N.431, H.453 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.4, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.4 No protein-ligand interaction detected (PLIP)

1 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(Non-functional Binders)

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.4: 22 residues within 4Å: Chain C: K.333, G.334, S.358, H.359, N.382, S.384, Y.385, L.404, D.406 Chain D: F.63, D.65, Y.78, S.79, Y.80, P.81, E.84, Y.126, E.128, N.129, R.130 Ligands: NAG-NAG.5, NAG-NAG.5 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:E.128, D:N.129 Water bridges: D:R.130, C:Y.385

1 x CU: COPPER (II) ION(Non-covalent)

CU.6: 2 residues within 4Å: Chain A: E.249, H.275 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.249, A:E.249, A:H.275

15 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 8 residues within 4Å: Chain A: L.176, A.179, T.180, N.181, L.182, A.202, V.203, F.204 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.179, A:L.182, A:V.203 Water bridges: A:N.181 GOL.8: 6 residues within 4Å: Chain A: N.335, K.337, H.359, D.360, D.361 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.337, A:D.361 Water bridges: A:D.361, A:D.361 GOL.9: 5 residues within 4Å: Chain A: G.525, S.547, Q.548, Q.549, K.578 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.578, A:K.578 GOL.10: 4 residues within 4Å: Chain A: H.509, N.510, S.532, H.534 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.532 GOL.11: 4 residues within 4Å: Chain A: H.434, Q.457, F.485 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.434 GOL.17: 5 residues within 4Å: Chain A: F.61, T.85, V.87, F.111 Chain B: R.96 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.96 Water bridges: B:D.58, B:D.58, B:D.58, B:D.58, A:T.85, A:T.85 GOL.18: 7 residues within 4Å: Chain A: I.113, G.137, D.159, Q.161, N.185 Chain B: G.94, R.96 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.96, B:R.96 Water bridges: A:G.137, A:D.159, A:D.159 GOL.19: 3 residues within 4Å: Chain B: G.7, W.8, P.28 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.7 GOL.22: 4 residues within 4Å: Chain C: S.489, R.511, T.513, H.534 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.489 Water bridges: C:R.511 GOL.23: 4 residues within 4Å: Chain C: H.453, I.480, V.482, H.504 2 PLIP interactions: 2 interactions with chain C Water bridges: C:H.504, C:H.504 GOL.24: 7 residues within 4Å: Chain A: S.118, H.140 Chain C: Q.114, S.138, N.162 Chain D: R.95, Q.100 8 PLIP interactions: 4 interactions with chain D, 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: D:R.95, D:Q.100, D:Y.102, C:Q.114, C:S.138, C:N.162, A:S.118 Water bridges: D:R.95 GOL.27: 4 residues within 4Å: Chain A: Y.70, W.71 Chain C: R.66, Q.68 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:R.66, A:W.71 GOL.30: 4 residues within 4Å: Chain C: F.61, V.87, F.111 Chain D: R.96 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:R.96 Water bridges: C:T.85 GOL.31: 7 residues within 4Å: Chain A: S.118, S.119 Chain C: D.237 Chain D: S.91, Y.102, Y.103, A.104 8 PLIP interactions: 4 interactions with chain D, 2 interactions with chain C, 2 interactions with chain A Hydrogen bonds: D:S.91, D:A.104, C:D.237, A:S.119, A:S.119 Water bridges: D:Y.102, D:A.104, C:D.237 GOL.32: 7 residues within 4Å: Chain A: Q.49, H.73, E.74 Chain D: P.9, K.10, H.11 Ligands: NAG.14 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:E.74, A:E.74, A:E.74, D:H.11 Water bridges: A:E.74

13 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.12: 2 residues within 4Å: Chain A: V.13, N.14 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.13 Hydrogen bonds: A:N.14 NAG.13: 2 residues within 4Å: Chain A: N.33, R.55 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.33 NAG.14: 5 residues within 4Å: Chain A: N.50, T.51, S.54, Q.78 Ligands: GOL.32 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.50, A:Q.78 NAG.15: 5 residues within 4Å: Chain A: N.224, S.225, T.226, E.253, S.255 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.224 NAG.16: 4 residues within 4Å: Chain A: E.347, N.348, E.350, N.374 3 PLIP interactions: 3 interactions with chain A Water bridges: A:S.376, A:S.376, A:S.376 NAG.20: 4 residues within 4Å: Chain B: S.74, I.75, L.76, N.77 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.74, B:S.74, B:N.77 Water bridges: B:N.77 NAG.21: 3 residues within 4Å: Chain B: C.26, L.122, N.137 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.122 Hydrogen bonds: B:N.137 NAG.25: 1 residues within 4Å: Chain C: N.14 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.14 NAG.26: 3 residues within 4Å: Chain C: G.29, N.33, R.55 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.33 Water bridges: C:S.54, C:R.55 NAG.28: 5 residues within 4Å: Chain C: N.224, S.225, T.226, E.253, S.255 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.224 NAG.29: 3 residues within 4Å: Chain C: E.347, E.350, N.374 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:E.347 Water bridges: C:S.376 NAG.33: 3 residues within 4Å: Chain D: S.74, I.75, N.77 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.74, D:S.74, D:N.77 NAG.34: 3 residues within 4Å: Chain D: K.10, Q.24, N.137 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.24

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ohto, U. et al., Crystal Structures of Mouse and Human RP105/MD-1 Complexes Reveal Unique Dimer Organization of the Toll-Like Receptor Family. J.Mol.Biol. (2011)

Release Date

2011-11-09

Peptides

CD180 antigen: AC
Lymphocyte antigen 86: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
B

B
C

D
D

CD180 antigen

Lymphocyte antigen 86