SMTL ID : 3cif.1 (4 other biounits)

Crystal Structure of C153S mutant glyceraldehyde 3-phosphate dehydrogenase from Cryptosporidium parvum

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

4 x G3H: GLYCERALDEHYDE-3-PHOSPHATE(Non-covalent)

G3H.1: 11 residues within 4Å: Chain A: S.172, S.173, T.174, H.200, T.203, T.234, G.235, A.236, R.257, N.339 Ligands: NAD.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.172, A:S.172, A:S.173, A:T.174, A:T.174, A:H.200, A:T.234, A:G.235, A:A.236, A:R.257, A:N.339 G3H.3: 11 residues within 4Å: Chain B: S.172, S.173, T.174, H.200, T.203, T.234, G.235, A.236, R.257, N.339 Ligands: NAD.4 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:S.172, B:S.173, B:S.173, B:T.174, B:T.174, B:T.174, B:H.200, B:T.234, B:G.235, B:A.236, B:R.257 Water bridges: B:S.233, B:S.233 G3H.9: 10 residues within 4Å: Chain C: S.172, S.173, T.174, H.200, T.203, T.234, A.236, R.257, N.339 Ligands: NAD.7 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:S.172, C:S.173, C:S.173, C:T.174, C:T.174, C:T.174, C:H.200, C:R.257 Water bridges: C:S.233 G3H.10: 10 residues within 4Å: Chain D: S.172, S.173, T.174, H.200, T.203, N.205, R.257, N.339 Ligands: NAD.11, MG.12 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:S.173, D:T.174, D:T.203, D:R.257 Salt bridges: D:H.200

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

NAD.2: 24 residues within 4Å: Chain A: N.28, G.29, F.30, G.31, R.32, I.33, N.53, D.54, P.55, F.56, M.57, A.98, K.99, S.117, T.118, G.119, F.121, S.141, A.142, S.173, A.204, N.339, Y.343 Ligands: G3H.1 18 PLIP interactions: 17 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:I.33, A:Y.343 Hydrogen bonds: A:F.30, A:F.30, A:R.32, A:I.33, A:N.53, A:K.99, A:N.339, A:N.339 Water bridges: A:N.28, A:N.28, A:G.31, A:G.34, A:R.35, A:G.119, A:S.141, D:D.210 NAD.4: 24 residues within 4Å: Chain B: N.28, G.29, F.30, G.31, R.32, I.33, N.53, D.54, P.55, F.56, M.57, A.98, K.99, S.117, T.118, G.119, F.121, S.141, A.142, S.173, A.204, N.339, Y.343 Ligands: G3H.3 20 PLIP interactions: 19 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:I.33, B:Y.343 Hydrogen bonds: B:N.28, B:F.30, B:R.32, B:I.33, B:N.53, B:K.99, B:N.339, B:N.339 Water bridges: B:G.31, B:G.34, B:R.35, B:G.119, B:S.141, B:A.204, B:A.204, B:N.205, C:D.210 pi-Stacking: B:F.56 NAD.7: 25 residues within 4Å: Chain C: N.28, G.29, F.30, G.31, R.32, I.33, N.53, D.54, P.55, F.56, M.57, A.98, K.99, S.117, T.118, G.119, F.121, S.141, A.142, S.173, A.204, N.339, Y.343 Ligands: GOL.8, G3H.9 17 PLIP interactions: 16 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:I.33, C:Y.343 Hydrogen bonds: C:N.28, C:F.30, C:R.32, C:I.33, C:N.53, C:K.99, C:N.339 Water bridges: C:G.31, C:G.34, C:R.35, C:G.119, C:S.141, C:A.204, C:A.204, B:D.210 NAD.11: 25 residues within 4Å: Chain A: P.212 Chain D: N.28, G.29, F.30, G.31, R.32, I.33, N.53, D.54, P.55, F.56, M.57, A.98, K.99, S.117, T.118, G.119, F.121, S.141, A.142, S.173, A.204, N.339, Y.343 Ligands: G3H.10 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:I.33, D:Y.343 Hydrogen bonds: D:N.28, D:F.30, D:R.32, D:I.33, D:N.53, D:K.99, D:N.339 Water bridges: D:G.31, D:G.34, D:G.119, D:S.141, D:A.204, D:A.204, D:A.204, D:E.340

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain B: D.308, F.309, C.312 Chain D: Y.68, N.74 No protein-ligand interaction detected (PLIP) GOL.8: 3 residues within 4Å: Chain B: P.212 Chain C: F.56 Ligands: NAD.7 No protein-ligand interaction detected (PLIP)

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 3 residues within 4Å: Chain B: C.41, R.44, I.47 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.41, B:R.44, B:I.47 MG.12: 4 residues within 4Å: Chain D: S.172, T.174, T.234 Ligands: G3H.10 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cook, W.J. et al., An unexpected phosphate binding site in Glyceraldehyde 3-Phosphate Dehydrogenase: Crystal structures of apo, holo and ternary complex of Cryptosporidium parvum enzyme. BMC STRUCT.BIOL. (2009)

Release Date

2009-03-24

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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