SMTL ID : 1gyp.1

CRYSTAL STRUCTURE OF GLYCOSOMAL GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM LEISHMANIA MEXICANA: IMPLICATIONS FOR STRUCTURE-BASED DRUG DESIGN AND A NEW POSITION FOR THE INORGANIC PHOSPHATE BINDING SITE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-tetramer

Ligands

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

PO4.1: 7 residues within 4Å: Chain A: S.165, C.166, T.167, H.194, T.226, G.227, A.228 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.165, A:T.167, A:T.167, A:T.226, A:T.226, A:G.227, A:A.228 Salt bridges: A:H.194 PO4.2: 4 residues within 4Å: Chain A: T.197, T.199, R.249 Ligands: NAD.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.197, A:T.199 Salt bridges: A:R.249 PO4.4: 7 residues within 4Å: Chain B: S.165, C.166, T.167, H.194, T.226, G.227, R.249 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.165, B:T.167, B:T.167, B:T.226, B:G.227, B:R.249 Salt bridges: B:H.194 PO4.5: 4 residues within 4Å: Chain B: T.197, T.199, R.249 Ligands: NAD.6 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.197, B:T.197, B:T.197, B:T.199 Salt bridges: B:R.249 PO4.7: 7 residues within 4Å: Chain C: S.165, C.166, T.167, H.194, T.226, G.227, A.228 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:S.165, C:T.167, C:T.167, C:T.225, C:T.226, C:G.227, C:A.228 Salt bridges: C:H.194 PO4.8: 4 residues within 4Å: Chain C: T.197, T.199, R.249 Ligands: NAD.9 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.197, C:T.197, C:T.197 Salt bridges: C:R.249 PO4.10: 7 residues within 4Å: Chain D: S.165, C.166, T.167, H.194, T.226, G.227, A.228 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:S.165, D:T.167, D:T.167, D:T.226, D:G.227, D:A.228 Salt bridges: D:H.194 PO4.11: 4 residues within 4Å: Chain D: T.197, T.199, R.249 Ligands: NAD.12 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.197 Salt bridges: D:R.249

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.3: 24 residues within 4Å: Chain A: N.8, G.9, F.10, G.11, R.12, I.13, V.37, D.38, M.39, A.90, Q.91, S.110, T.111, G.112, L.113, S.134, A.135, C.166, T.197, A.198, N.335, Y.339 Chain B: V.206 Ligands: PO4.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.13, A:Y.339 Hydrogen bonds: A:N.8, A:F.10, A:R.12, A:I.13, A:D.38, A:Q.91, A:N.335 NAD.6: 24 residues within 4Å: Chain A: V.206 Chain B: N.8, G.9, F.10, G.11, R.12, I.13, V.37, D.38, M.39, A.90, Q.91, S.110, T.111, G.112, L.113, S.134, A.135, C.166, T.197, A.198, N.335, Y.339 Ligands: PO4.5 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.13, B:Y.339 Hydrogen bonds: B:N.8, B:R.12, B:I.13, B:Q.91, B:N.335 NAD.9: 23 residues within 4Å: Chain C: N.8, G.9, G.11, R.12, I.13, V.37, D.38, M.39, A.90, Q.91, S.110, T.111, G.112, L.113, S.134, A.135, C.166, T.197, A.198, N.335, Y.339 Chain D: V.206 Ligands: PO4.8 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:I.13, C:I.13, C:Y.339 Hydrogen bonds: C:N.8, C:R.12, C:I.13, C:Q.91, C:N.335 NAD.12: 25 residues within 4Å: Chain C: V.206 Chain D: N.8, G.9, F.10, G.11, R.12, I.13, V.37, D.38, M.39, A.90, Q.91, S.110, T.111, G.112, L.113, F.114, S.134, A.135, C.166, A.198, N.335, E.336, Y.339 Ligands: PO4.11 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:I.13, D:I.13, D:Y.339 Hydrogen bonds: D:N.8, D:F.10, D:R.12, D:I.13, D:Q.91, D:N.335

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, H. et al., Crystal structure of glycosomal glyceraldehyde-3-phosphate dehydrogenase from Leishmania mexicana: implications for structure-based drug design and a new position for the inorganic phosphate binding site. Biochemistry (1995)

Release Date

1995-12-07

Peptides

GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE

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