SMTL ID : 2ag2.3 (2 other biounits)

Crystal Structure Analysis of GM2-activator protein complexed with Phosphatidylcholine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

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

CL.1: 6 residues within 4Å: Chain A: S.49, P.50, L.51, H.81, F.82, C.83 Ligand excluded by PLIP

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

EPE.2: 4 residues within 4Å: Chain A: S.6, W.7, D.8, E.12 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:W.7 Water bridges: A:N.9, A:N.9, A:R.20 Salt bridges: A:D.8, A:D.8, A:E.12

1 x CH5: 2-(((R)-2,3-DIHYDROXYPROPYL)PHOSPHORYLOXY)-N,N,N-TRIMETHYLETHANAMINIUM(Non-covalent)

CH5.3: 7 residues within 4Å: Chain A: Y.73, F.79, F.82, V.85, M.88, L.89 Ligands: MYR.6 No protein-ligand interaction detected (PLIP)

1 x LP3: (7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE(Non-covalent)

LP3.4: 21 residues within 4Å: Chain A: A.17, V.18, I.19, G.41, S.42, L.47, V.53, L.86, L.100, P.106, Y.116, S.143, V.144, L.145, G.153, C.154, I.155 Ligands: OLA.5, MYR.6, IPA.7, IPA.9 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.47, A:L.100, A:Y.116, A:Y.116 Hydrogen bonds: A:S.143, A:G.153

1 x OLA: OLEIC ACID(Non-covalent)

OLA.5: 15 residues within 4Å: Chain A: I.19, L.24, L.37, V.39, G.41, Y.116, S.117, L.118, I.141, I.157, A.159 Ligands: LP3.4, MYR.6, IPA.8, IPA.9 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.19, A:L.24, A:L.37, A:V.39, A:Y.116, A:L.118, A:I.141, A:I.157

1 x MYR: MYRISTIC ACID(Non-covalent)

MYR.6: 5 residues within 4Å: Chain A: F.123, V.125 Ligands: CH5.3, LP3.4, OLA.5 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.123

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

IPA.7: 2 residues within 4Å: Chain A: L.51 Ligands: LP3.4 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.51 IPA.8: 7 residues within 4Å: Chain A: L.57, W.133, L.134, Y.139, L.161 Ligands: OLA.5, IPA.11 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.57, A:W.133, A:L.134, A:Y.139 IPA.9: 3 residues within 4Å: Chain A: L.55 Ligands: LP3.4, OLA.5 No protein-ligand interaction detected (PLIP) IPA.10: 2 residues within 4Å: Chain A: L.100, L.118 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.100, A:L.118 IPA.11: 6 residues within 4Å: Chain A: L.55, L.57, Y.73, I.74, G.75 Ligands: IPA.8 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.55, A:L.57 Hydrogen bonds: A:Y.73, A:G.75

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wright, C.S. et al., Crystal Structure Analysis of Phosphatidylcholine-GM2-Activator Product Complexes: Evidence for Hydrolase Activity. Biochemistry (2005)

Release Date

2005-10-25

Peptides

Ganglioside GM2 activator: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

Ganglioside GM2 activator

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