SMTL ID : 1tjj.6 (5 other biounits)

Human GM2 Activator Protein PAF complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

ACT.1: 6 residues within 4Å: Chain A: L.47, F.111, L.145 Ligands: ACT.2, PFS.4, LPE.5 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.47, A:L.145 ACT.2: 3 residues within 4Å: Chain A: C.107 Ligands: ACT.1, LPE.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.106 ACT.8: 4 residues within 4Å: Chain B: L.47, L.51, F.111 Ligands: LPE.13 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.47, B:L.51, B:F.111 ACT.9: 6 residues within 4Å: Chain B: I.141, S.143, I.155, I.157 Ligands: PFS.12, LPE.13 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.141, B:I.157 Hydrogen bonds: B:S.143

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

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

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

PFS.4: 21 residues within 4Å: Chain A: 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.1, LPE.5, DAO.6 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.37, A:V.39, A:V.39, A:Y.116, A:I.141, A:I.157, A:I.157, A:A.159 PFS.12: 20 residues within 4Å: Chain A: W.133 Chain B: 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.9, LPE.13, IPA.14 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.19, B:Y.116, B:L.118, B:I.141, B:I.157, B:I.157, B:A.159

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

LPE.5: 21 residues within 4Å: Chain A: 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.1, ACT.2, PFS.4, DAO.6 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.39, A:L.100, A:P.106, A:F.111, A:Y.116, A:Y.116, A:L.118 Hydrogen bonds: A:S.143 LPE.13: 23 residues within 4Å: Chain B: 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.8, ACT.9, PFS.12 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.79, B:F.82, B:L.89, B:I.90, B:F.111, B:F.111, B:F.111 Hydrogen bonds: B:L.145, B:I.155

1 x DAO: LAURIC ACID(Non-covalent)

DAO.6: 7 residues within 4Å: Chain A: I.29, V.35, P.97, F.123, V.125 Ligands: PFS.4, LPE.5 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.29, A:V.35, A:P.97, A:F.123, A:F.123, A:F.123

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

IPA.7: 2 residues within 4Å: Chain A: P.110, K.112 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.110, A:K.112 Water bridges: A:K.112 IPA.14: 2 residues within 4Å: Chain B: V.35 Ligands: PFS.12 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.35

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

EPE.11: 4 residues within 4Å: Chain B: S.6, W.7, D.8, E.12 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:W.7, B:W.7 Water bridges: B:E.12 Salt bridges: B:D.8, B:D.8, B:E.12

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Ganglioside GM2 activator

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