SMTL ID : 4g8a.1

Crystal structure of human TLR4 polymorphic variant D299G and T399I in complex with MD-2 and LPS

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-2-2-mer

Ligands

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

NAG-NAG.1: 8 residues within 4Å: Chain A: S.502, Q.503, N.524, S.526, V.546, D.548 Ligands: NAG-NAG.2, NAG-NAG.2 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 9 residues within 4Å: Chain A: V.546, D.548, S.550, L.551, N.573, V.600, R.604 Ligands: NAG-NAG.1, NAG-NAG.1 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 8 residues within 4Å: Chain B: S.502, Q.503, N.524, V.546, D.548, L.551 Ligands: NAG-NAG.4, NAG-NAG.4 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.551 NAG-NAG.4: 10 residues within 4Å: Chain B: S.526, V.546, D.548, S.550, L.551, F.571, N.573, V.600 Ligands: NAG-NAG.3, NAG-NAG.3 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.546, B:F.571

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

NAG.5: 3 residues within 4Å: Chain A: G.145, H.146, N.171 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.171 NAG.6: 4 residues within 4Å: Chain B: G.145, H.146, K.148, N.171 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.148, B:K.148 NAG.7: 2 residues within 4Å: Chain C: F.48, N.98 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.48 Hydrogen bonds: C:N.98 NAG.13: 2 residues within 4Å: Chain D: F.48, N.98 No protein-ligand interaction detected (PLIP)

2 x LP4: 2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-4-O-phosphono-beta-D-glucopyranose(Non-covalent)

LP4.8: 15 residues within 4Å: Chain A: R.262 Chain C: I.47, Y.49, F.60, Y.86, F.88, I.101, S.102, F.103, S.104, F.135 Ligands: LP5.9, DAO.10, MYR.11, KDO.12 13 PLIP interactions: 11 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:I.47, C:Y.49, C:F.60, C:F.88, C:I.101, C:I.101, C:F.135 Hydrogen bonds: C:S.102, C:S.102, C:S.104, C:S.104 Salt bridges: A:R.262, A:R.262 LP4.14: 15 residues within 4Å: Chain B: R.262 Chain D: L.45, I.47, F.60, Y.86, F.88, I.101, S.102, F.103, S.104, F.105 Ligands: LP5.15, DAO.16, MYR.17, KDO.18 13 PLIP interactions: 11 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:L.45, D:I.47, D:F.60, D:F.60, D:F.88, D:I.101, D:F.103 Hydrogen bonds: D:S.102, D:S.102, D:S.104, D:S.104 Salt bridges: B:R.262, B:R.262

2 x LP5: (R)-((2R,3S,4R,5R,6R)-3-HYDROXY-2-(HYDROXYMETHYL)-5-((R)-3-HYDROXYTETRADECANAMIDO)-6-(PHOSPHONOOXY)TETRAHYDRO-2H-PYRAN-4-YL) 3-HYDROXYTETRADECANOATE(Non-covalent)

LP5.9: 18 residues within 4Å: Chain B: S.413, Q.434, E.437, F.438 Chain C: I.36, L.38, I.64, V.66, L.71, R.74, F.105, K.106, I.108, F.110, F.135 Ligands: LP4.8, DAO.10, MYR.11 18 PLIP interactions: 14 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:I.36, C:L.38, C:I.64, C:V.66, C:L.71, C:F.105, C:F.105, C:F.105, C:F.110, C:F.110, C:F.135, B:F.438, B:F.438 Hydrogen bonds: C:K.106, C:K.106, C:K.106, B:S.413, B:Q.434 LP5.15: 15 residues within 4Å: Chain A: S.413, Q.434, E.437, F.438 Chain D: V.66, L.71, R.74, F.105, K.106, I.108, F.110, F.135 Ligands: LP4.14, DAO.16, MYR.17 16 PLIP interactions: 13 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:V.66, D:L.71, D:F.105, D:F.105, D:F.105, D:I.108, D:F.110, D:F.110, D:F.135, A:F.438 Hydrogen bonds: D:K.106, D:K.106, D:K.106, D:I.108, A:S.413, A:Q.434

2 x DAO: LAURIC ACID(Non-covalent)

DAO.10: 11 residues within 4Å: Chain C: L.38, L.62, I.64, R.74, E.76, F.110, Y.115, I.137 Ligands: LP4.8, LP5.9, MYR.11 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:L.38, C:L.62, C:I.64, C:F.110, C:Y.115, C:I.137 DAO.16: 7 residues within 4Å: Chain D: L.62, R.74, Y.115, I.137 Ligands: LP4.14, LP5.15, MYR.17 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:L.62, D:Y.115, D:Y.115, D:I.137

2 x MYR: MYRISTIC ACID(Non-covalent)

MYR.11: 6 residues within 4Å: Chain C: I.47, F.60, E.76 Ligands: LP4.8, LP5.9, DAO.10 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:I.47, C:F.60, C:F.60 MYR.17: 9 residues within 4Å: Chain D: I.30, I.47, F.60, L.62, E.76, Y.86 Ligands: LP4.14, LP5.15, DAO.16 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:I.30, D:I.47, D:F.60, D:L.62 Hydrogen bonds: D:Y.86

2 x KDO: 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid(Non-covalent)

KDO.12: 3 residues within 4Å: Chain A: Y.294, K.339 Ligands: LP4.8 No protein-ligand interaction detected (PLIP) KDO.18: 4 residues within 4Å: Chain B: Y.294, K.339 Chain D: K.106 Ligands: LP4.14 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:Y.294, D:K.106

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ohto, U. et al., Structural analyses of human Toll-like receptor 4 polymorphisms D299G and T399I. J.Biol.Chem. (2012)

Release Date

2012-10-17

Peptides

Toll-like receptor 4: AB
Lymphocyte antigen 96: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Toll-like receptor 4

Lymphocyte antigen 96

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