SMTL ID : 3fxi.1

Crystal structure of the human TLR4-human MD-2-E.coli LPS Ra complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

hetero-2-2-mer

Ligands

1 x PA1- PA1- KDO- GMH- GMH- GMH- KDO: L-glycero-alpha-D-manno-heptopyranose-(1-7)-L-glycero-alpha-D-manno-heptopyranose-(1-3)-L-glycero-alpha-D-manno-heptopyranose-(1-5)-[3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)]3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-amino-2-deoxy-alpha-D-glucopyranose-(1-6)-2-amino-2-deoxy-alpha-D-glucopyranose

PA1-PA1-KDO-GMH-GMH-GMH-KDO.1: 17 residues within 4Å: Chain A: D.268, Y.270, K.315, K.336 Chain C: K.40, S.102, F.103, K.104 Ligands: FTT.7, FTT.8, FTT.9, FTT.10, PO4.13, PO4.14, PO4.15, PO4.16, MG.20 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:D.268, C:S.102, C:S.102, C:S.102, C:S.102

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.2: 6 residues within 4Å: Chain A: S.478, Q.479, N.500, D.524 Ligands: NAG-NAG.3, NAG-NAG.3 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 9 residues within 4Å: Chain A: V.522, D.524, S.526, F.547, N.549, T.551, R.580 Ligands: NAG-NAG.2, NAG-NAG.2 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 7 residues within 4Å: Chain B: S.478, Q.479, N.500, S.502, D.524 Ligands: NAG-NAG.6, NAG-NAG.6 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 11 residues within 4Å: Chain B: V.522, D.524, S.526, F.547, N.549, T.551, V.576, E.577, R.580 Ligands: NAG-NAG.5, NAG-NAG.5 No protein-ligand interaction detected (PLIP)

1 x PA1- GCS- KDO- GMH- GMH- GMH- KDO: L-glycero-alpha-D-manno-heptopyranose-(1-7)-L-glycero-alpha-D-manno-heptopyranose-(1-3)-L-glycero-alpha-D-manno-heptopyranose-(1-5)-[3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)]3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-amino-2-deoxy-beta-D-glucopyranose-(1-6)-2-amino-2-deoxy-alpha-D-glucopyranose

PA1-GCS-KDO-GMH-GMH-GMH-KDO.4: 18 residues within 4Å: Chain B: D.268, Y.270, K.315, K.336 Chain D: K.40, F.101, S.102, F.103, K.104 Ligands: FTT.21, FTT.22, FTT.23, FTT.24, PO4.27, PO4.28, PO4.29, PO4.30, MG.34 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:D.268, D:S.102, D:K.104, D:K.104, D:S.102, D:S.102

8 x FTT: 3-HYDROXY-TETRADECANOIC ACID(Non-covalent)

FTT.7: 13 residues within 4Å: Chain B: S.389, Q.410, E.413, F.414 Chain C: V.64, L.69, R.72, I.106, F.108, S.109, Y.113 Ligands: PA1-PA1-KDO-GMH-GMH-GMH-KDO.1, DAO.11 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:F.414, C:V.64, C:V.64, C:L.69, C:I.106, C:Y.113 Hydrogen bonds: B:Q.410, B:E.413 FTT.8: 9 residues within 4Å: Chain C: F.103, K.104, I.106, F.108, C.115, F.133 Ligands: PA1-PA1-KDO-GMH-GMH-GMH-KDO.1, DAO.11, MYR.12 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:F.103, C:F.103, C:F.103, C:F.108, C:F.133, C:F.133 Hydrogen bonds: C:K.104, C:I.106 FTT.9: 11 residues within 4Å: Chain C: V.6, I.14, V.30, F.101, S.102, F.133 Ligands: PA1-PA1-KDO-GMH-GMH-GMH-KDO.1, PA1-PA1-KDO-GMH-GMH-GMH-KDO.1, FTT.10, DAO.11, MYR.12 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:V.6, C:I.14, C:V.30, C:F.101, C:F.133 FTT.10: 16 residues within 4Å: Chain A: R.238 Chain C: L.43, I.45, Y.47, L.53, L.56, F.58, Y.84, F.86, I.99, S.100, F.101 Ligands: PA1-PA1-KDO-GMH-GMH-GMH-KDO.1, FTT.9, MYR.12, PO4.13 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:L.43, C:Y.47, C:L.53, C:L.56, C:F.58, C:F.86, C:I.99, C:I.99, C:F.101 Hydrogen bonds: C:Y.84 FTT.21: 13 residues within 4Å: Chain A: S.389, Q.410, E.413, F.414 Chain D: V.64, L.69, R.72, I.106, F.108, S.109, Y.113 Ligands: PA1-GCS-KDO-GMH-GMH-GMH-KDO.4, DAO.25 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:V.64, D:V.64, D:L.69, D:I.106, D:Y.113, A:F.414 Hydrogen bonds: A:Q.410 FTT.22: 8 residues within 4Å: Chain D: F.103, K.104, I.106, F.108, C.115, F.133 Ligands: PA1-GCS-KDO-GMH-GMH-GMH-KDO.4, DAO.25 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:F.103, D:F.103, D:F.103, D:F.108, D:F.133, D:F.133 Hydrogen bonds: D:K.104, D:K.104, D:I.106 FTT.23: 11 residues within 4Å: Chain D: V.6, I.14, V.30, F.101, S.102, F.133 Ligands: PA1-GCS-KDO-GMH-GMH-GMH-KDO.4, PA1-GCS-KDO-GMH-GMH-GMH-KDO.4, FTT.24, DAO.25, MYR.26 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:V.6, D:I.14, D:V.30, D:F.101, D:F.133 FTT.24: 16 residues within 4Å: Chain B: R.238 Chain D: L.43, I.45, Y.47, L.53, L.56, F.58, Y.84, F.86, I.99, S.100, F.101 Ligands: PA1-GCS-KDO-GMH-GMH-GMH-KDO.4, FTT.23, MYR.26, PO4.27 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:L.43, D:Y.47, D:L.53, D:L.56, D:F.58, D:F.86, D:I.99, D:I.99, D:F.101 Hydrogen bonds: D:Y.84

2 x DAO: LAURIC ACID(Non-covalent)

DAO.11: 9 residues within 4Å: Chain C: L.36, L.60, I.62, R.72, Y.113 Ligands: FTT.7, FTT.8, FTT.9, MYR.12 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.36, C:L.60, C:I.62, C:Y.113, C:Y.113 DAO.25: 10 residues within 4Å: Chain D: L.36, L.60, I.62, R.72, E.74, Y.113 Ligands: FTT.21, FTT.22, FTT.23, MYR.26 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:L.36, D:L.60, D:I.62, D:Y.113, D:Y.113

2 x MYR: MYRISTIC ACID(Non-covalent)

MYR.12: 8 residues within 4Å: Chain C: I.28, I.45, F.58, E.74 Ligands: FTT.8, FTT.9, FTT.10, DAO.11 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:I.28, C:I.45, C:F.58, C:F.58 MYR.26: 7 residues within 4Å: Chain D: I.28, I.45, F.58, E.74 Ligands: FTT.23, FTT.24, DAO.25 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:I.28, D:I.45, D:F.58, D:F.58

8 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.13: 5 residues within 4Å: Chain A: R.238 Chain C: S.100 Ligands: PA1-PA1-KDO-GMH-GMH-GMH-KDO.1, FTT.10, MG.20 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain C Salt bridges: A:R.238 Hydrogen bonds: C:S.100, C:S.100 Water bridges: C:S.100 PO4.14: 2 residues within 4Å: Ligands: PA1-PA1-KDO-GMH-GMH-GMH-KDO.1, PA1-PA1-KDO-GMH-GMH-GMH-KDO.1 No protein-ligand interaction detected (PLIP) PO4.15: 2 residues within 4Å: Chain A: R.296 Ligands: PA1-PA1-KDO-GMH-GMH-GMH-KDO.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.296 PO4.16: 3 residues within 4Å: Chain B: E.343 Ligands: PA1-PA1-KDO-GMH-GMH-GMH-KDO.1, PA1-PA1-KDO-GMH-GMH-GMH-KDO.1 No protein-ligand interaction detected (PLIP) PO4.27: 5 residues within 4Å: Chain B: R.238 Chain D: S.100 Ligands: PA1-GCS-KDO-GMH-GMH-GMH-KDO.4, FTT.24, MG.34 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:S.100, D:S.100 Water bridges: D:S.100 Salt bridges: B:R.238 PO4.28: 2 residues within 4Å: Ligands: PA1-GCS-KDO-GMH-GMH-GMH-KDO.4, PA1-GCS-KDO-GMH-GMH-GMH-KDO.4 No protein-ligand interaction detected (PLIP) PO4.29: 2 residues within 4Å: Chain B: R.296 Ligands: PA1-GCS-KDO-GMH-GMH-GMH-KDO.4 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.296 PO4.30: 3 residues within 4Å: Chain A: E.343 Ligands: PA1-GCS-KDO-GMH-GMH-GMH-KDO.4, PA1-GCS-KDO-GMH-GMH-GMH-KDO.4 No protein-ligand interaction detected (PLIP)

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

NAG.17: 3 residues within 4Å: Chain A: G.121, H.122, N.147 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.122, A:N.147, A:N.147 NAG.18: 5 residues within 4Å: Chain A: E.152, H.153, N.179, S.181, H.203 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.152, A:N.179 NAG.19: 2 residues within 4Å: Chain A: S.446, N.471 No protein-ligand interaction detected (PLIP) NAG.31: 2 residues within 4Å: Chain B: Y.144, N.147 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.147 NAG.32: 4 residues within 4Å: Chain B: E.152, H.153, N.179, H.203 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.152 NAG.33: 3 residues within 4Å: Chain B: S.445, S.446, N.471 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.471 NAG.35: 2 residues within 4Å: Chain C: F.46, N.96 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.46 Hydrogen bonds: C:N.96 NAG.36: 2 residues within 4Å: Chain D: F.46, N.96 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.96

2 x MG: MAGNESIUM ION(Non-covalent)

MG.20: 3 residues within 4Å: Chain A: D.268 Ligands: PA1-PA1-KDO-GMH-GMH-GMH-KDO.1, PO4.13 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.268, H2O.1 MG.34: 3 residues within 4Å: Chain B: D.268 Ligands: PA1-GCS-KDO-GMH-GMH-GMH-KDO.4, PO4.27 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Park, B.S. et al., The structural basis of lipopolysaccharide recognition by the TLR4-MD-2 complex. Nature (2009)

Release Date

2009-03-03

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