SMTL ID : 2ag2.2 (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 CH5: 2-(((R)-2,3-DIHYDROXYPROPYL)PHOSPHORYLOXY)-N,N,N-TRIMETHYLETHANAMINIUM(Non-covalent)

CH5.2: 12 residues within 4Å: Chain A: L.57, K.59, I.68, I.74, L.128, L.130, L.134, Y.139, L.161 Ligands: OLA.4, DAO.6, IPA.8 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)

LP3.3: 27 residues within 4Å: Chain A: A.17, V.18, I.19, L.37, V.39, G.41, S.42, L.47, V.53, F.82, P.97, L.100, P.106, F.111, Y.116, F.123, S.143, V.144, L.145, G.153, C.154, I.155 Ligands: OLA.4, MYR.5, DAO.6, IPA.7, IPA.9 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.37, A:V.39, A:L.47, A:P.97, A:F.111, A:F.111, A:Y.116, A:Y.116 Hydrogen bonds: A:S.143, A:G.153

1 x OLA: OLEIC ACID(Non-covalent)

OLA.4: 17 residues within 4Å: Chain A: I.19, L.24, L.37, V.39, V.40, G.41, L.105, Y.116, S.117, L.118, I.155, I.157 Ligands: CH5.2, LP3.3, MYR.5, DAO.6, IPA.7 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.37, A:L.105, A:Y.116, A:L.118, A:I.155, A:I.157

1 x MYR: MYRISTIC ACID(Non-covalent)

MYR.5: 8 residues within 4Å: Chain A: L.55, Y.73, F.79, L.89, I.141 Ligands: LP3.3, OLA.4, IPA.8 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.55, A:Y.73, A:Y.73, A:F.79, A:I.141 Water bridges: A:D.72, A:D.72

1 x DAO: LAURIC ACID(Non-covalent)

DAO.6: 11 residues within 4Å: Chain A: I.29, V.35, I.74, F.123, V.125, P.126, L.128 Ligands: CH5.2, LP3.3, OLA.4, IPA.8 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.29, A:V.35, A:I.74, A:V.125, A:P.126, A:P.126, A:L.128

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

IPA.7: 7 residues within 4Å: Chain A: L.47, L.51, F.111, L.145 Ligands: LP3.3, OLA.4, IPA.9 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.47, A:L.51, A:F.111, A:L.145 IPA.8: 6 residues within 4Å: Chain A: I.74, G.75, I.141 Ligands: CH5.2, MYR.5, DAO.6 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.141 Hydrogen bonds: A:G.75, A:G.75 IPA.9: 4 residues within 4Å: Chain A: C.107, F.111 Ligands: LP3.3, IPA.7 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.111

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
B

Ganglioside GM2 activator

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