SMTL ID : 1tjj.4 (5 other biounits)

Human GM2 Activator Protein PAF complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-trimer

Ligands

5 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 4 residues within 4Å: Chain A: L.47, L.51, F.111 Ligands: LPE.6 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.47, A:L.51, A:F.111 ACT.2: 6 residues within 4Å: Chain A: I.141, S.143, I.155, I.157 Ligands: PFS.5, LPE.6 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.141, A:I.157 Hydrogen bonds: A:S.143 ACT.8: 6 residues within 4Å: Chain B: L.47, F.111, L.145 Ligands: ACT.9, PFS.11, LPE.12 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.47, B:L.145 ACT.9: 3 residues within 4Å: Chain B: C.107 Ligands: ACT.8, LPE.12 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.106 ACT.15: 4 residues within 4Å: Chain C: L.51, F.111 Ligands: PFS.18, LPE.19 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.51, C:F.111

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

CL.3: 7 residues within 4Å: Chain A: S.49, P.50, L.51, H.81, F.82, C.83, D.84 Ligand excluded by PLIP CL.10: 6 residues within 4Å: Chain B: S.49, P.50, L.51, H.81, F.82, C.83 Ligand excluded by PLIP CL.16: 6 residues within 4Å: Chain C: S.49, P.50, L.51, H.81, F.82, C.83 Ligand excluded by PLIP

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.4: 4 residues within 4Å: Chain A: S.6, W.7, D.8, E.12 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.7, A:W.7 Salt bridges: A:D.8, A:D.8, A:E.12 EPE.17: 5 residues within 4Å: Chain C: S.6, W.7, D.8, N.9, E.12 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:W.7, C:N.9, C:E.12 Water bridges: C:L.22 Salt bridges: C:D.8, C:D.8 pi-Cation interactions: C:W.7

3 x PFS: (2R)-2-(acetyloxy)-3-(hexadecyloxy)propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

PFS.5: 19 residues within 4Å: Chain A: I.19, L.24, V.39, L.57, I.68, Y.116, S.117, L.118, L.130, Y.139, R.140, I.141, I.157, A.158, A.159, L.161 Ligands: ACT.2, LPE.6, IPA.7 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.19, A:Y.116, A:L.118, A:I.141, A:I.157, A:I.157, A:A.159 PFS.11: 21 residues within 4Å: Chain B: I.19, L.24, L.37, V.39, G.41, L.57, I.68, I.74, Y.116, L.128, L.130, Y.139, R.140, I.141, I.157, A.158, A.159, L.161 Ligands: ACT.8, LPE.12, DAO.13 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.37, B:V.39, B:V.39, B:Y.116, B:I.141, B:I.157, B:I.157, B:A.159 PFS.18: 22 residues within 4Å: Chain C: I.19, L.22, L.24, L.37, V.39, L.57, I.68, Y.116, L.128, L.130, T.135, Y.139, R.140, I.141, I.157, A.158, A.159, L.161 Ligands: ACT.15, LPE.19, IPA.21, IPA.22 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:I.19, C:L.22, C:L.37, C:V.39, C:L.57, C:Y.116, C:Y.139, C:I.141, C:I.157 Hydrogen bonds: C:I.141

3 x LPE: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

LPE.6: 23 residues within 4Å: Chain A: A.17, V.18, I.19, G.41, S.42, V.53, L.55, F.79, F.82, L.86, L.89, I.90, P.106, F.111, Y.116, S.143, L.145, G.153, C.154, I.155 Ligands: ACT.1, ACT.2, PFS.5 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.79, A:F.82, A:L.89, A:I.90, A:F.111, A:F.111, A:F.111 Hydrogen bonds: A:L.145, A:I.155 LPE.12: 21 residues within 4Å: Chain B: A.17, V.18, I.19, V.39, G.41, S.42, V.53, F.82, L.100, P.106, F.111, Y.116, L.118, S.143, V.144, L.145, I.155 Ligands: ACT.8, ACT.9, PFS.11, DAO.13 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.39, B:L.100, B:P.106, B:F.111, B:Y.116, B:Y.116, B:L.118 Hydrogen bonds: B:S.143 LPE.19: 19 residues within 4Å: Chain C: A.17, V.18, I.19, G.41, S.42, V.53, F.82, L.86, P.106, F.111, Y.116, S.143, L.145, G.153, C.154, I.155 Ligands: ACT.15, PFS.18, IPA.21 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:L.86, C:F.111, C:F.111, C:Y.116 Hydrogen bonds: C:S.143, C:I.155

5 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.7: 2 residues within 4Å: Chain A: V.35 Ligands: PFS.5 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.35 IPA.14: 2 residues within 4Å: Chain B: P.110, K.112 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:P.110, B:K.112 Water bridges: B:K.112 IPA.20: 2 residues within 4Å: Chain C: Y.73, F.79 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.73, C:F.79 IPA.21: 3 residues within 4Å: Chain C: L.37 Ligands: PFS.18, LPE.19 No protein-ligand interaction detected (PLIP) IPA.22: 2 residues within 4Å: Chain C: P.126 Ligands: PFS.18 No protein-ligand interaction detected (PLIP)

1 x DAO: LAURIC ACID(Non-covalent)

DAO.13: 7 residues within 4Å: Chain B: I.29, V.35, P.97, F.123, V.125 Ligands: PFS.11, LPE.12 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.29, B:V.35, B:P.97, B:F.123, B:F.123, B:F.123

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wright, C.S. et al., Evidence for lipid packaging in the crystal structure of the GM2-activator complex with platelet activating factor. J.Mol.Biol. (2004)

Release Date

2004-12-07

Peptides

Ganglioside GM2 activator: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Ganglioside GM2 activator

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