SMTL ID : 1a7k.1

GLYCOSOMAL GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE IN A MONOCLINIC CRYSTAL FORM

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: 9 residues within 4Å: Chain A: S.165, C.166, T.167, H.194, T.225, T.226, G.227, A.228, R.249 9 PLIP interactions: 9 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, A:R.249 Salt bridges: A:H.194 PO4.2: 4 residues within 4Å: Chain A: T.197, T.199, R.249 Ligands: NAD.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.197, A:T.197, A:T.199, A:T.199 Salt bridges: A:R.249 PO4.4: 8 residues within 4Å: Chain B: S.165, C.166, T.167, H.194, T.225, T.226, G.227, A.228 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.165, B:C.166, B:T.167, B:T.167, B:T.226, B:T.226, B:G.227, B:A.228 Salt bridges: B:H.194 PO4.5: 3 residues within 4Å: Chain B: T.197, T.199 Ligands: NAD.6 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.197, B:T.197, B:T.197, B:T.199 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:C.166, C:T.167, C:T.167, 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 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.197, C:T.197 Salt bridges: C:R.249 PO4.10: 8 residues within 4Å: Chain D: S.165, C.166, T.167, T.168, H.194, T.226, G.227, A.228 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:S.165, D:C.166, D:T.167, D:T.167, D:T.168, 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 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.197, 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, 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, E.336, Y.339 Chain B: V.206 Ligands: PO4.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.13, A:I.13, A:Y.339 Hydrogen bonds: A:N.8, A:R.12, A:I.13, A:Q.91, A:N.335, A:E.336 NAD.6: 22 residues within 4Å: 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, A.198, N.335, Y.339 Ligands: PO4.5 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.13 Hydrogen bonds: B:F.10, B:R.12, B:I.13, B:Q.91, B:R.92, B:N.335 NAD.9: 24 residues within 4Å: Chain C: 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, A.198, N.335, E.336, Y.339 Chain D: V.206 Ligands: PO4.8 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:I.13, C:I.13, C:Y.339 Hydrogen bonds: C:N.8, C:F.10, C:R.12, C:I.13, C:Q.91, C:N.335, C:E.336, C:E.336 NAD.12: 23 residues within 4Å: Chain C: V.206 Chain D: 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, A.198, N.335, E.336, Y.339 Ligands: PO4.11 11 PLIP interactions: 11 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, D:E.336, D:E.336

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, H. et al., Crystal structure of Leishmania mexicana glycosomal glyceraldehyde-3-phosphate dehydrogenase in a new crystal form confirms the putative physiological active site structure. J.Mol.Biol. (1998)

Release Date

1998-06-17

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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