SMTL ID : 4qx6.1

CRYSTAL STRUCTURE OF GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM STREPTOCOCCUS AGALACTIAE NEM316 at 2.46 ANGSTROM RESOLUTION

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.46 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 23 residues within 4Å: Chain A: N.28, G.29, F.30, G.31, R.32, I.33, N.53, D.54, L.55, E.97, R.98, A.116, T.117, G.118, F.119, F.120, T.141, A.142, C.172, T.202, N.336, Y.340 Chain B: P.211 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.33, A:Y.340 Hydrogen bonds: A:F.30, A:R.32, A:I.33, A:R.98, A:T.141, A:N.336 Water bridges: A:N.28, A:G.31, A:G.34, A:G.118, A:T.141 NAD.2: 23 residues within 4Å: Chain A: P.211 Chain B: N.28, G.29, F.30, G.31, R.32, I.33, N.53, D.54, L.55, E.97, R.98, A.116, T.117, G.118, F.119, F.120, T.141, A.142, C.172, T.202, N.336, Y.340 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.33, B:I.33, B:Y.340 Hydrogen bonds: B:F.30, B:R.32, B:I.33, B:N.53, B:R.98, B:N.336 Water bridges: B:N.28, B:N.28, B:G.31, B:G.203, B:G.203, B:E.337, A:D.209 NAD.3: 24 residues within 4Å: Chain C: N.28, G.29, F.30, G.31, R.32, I.33, N.53, D.54, L.55, E.97, R.98, A.116, T.117, G.118, F.119, F.120, T.141, A.142, C.172, T.202, N.336, Y.340 Chain D: P.211 Ligands: EDO.4 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:I.33, C:Y.340 Hydrogen bonds: C:F.30, C:R.32, C:I.33, C:N.53, C:R.98, C:T.141, C:N.336 Water bridges: C:G.31, C:G.34 NAD.6: 23 residues within 4Å: Chain C: P.211 Chain D: N.28, G.29, F.30, G.31, R.32, I.33, N.53, D.54, L.55, E.97, R.98, A.116, T.117, G.118, F.119, F.120, T.141, A.142, C.172, T.202, N.336, Y.340 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:I.33, D:Y.340 Hydrogen bonds: D:F.30, D:R.32, D:I.33, D:N.53, D:R.98, D:N.336 Water bridges: D:N.28, D:N.28, D:G.31, D:G.118, D:T.141

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 11 residues within 4Å: Chain C: E.115, A.116, T.117, G.118, F.119, F.120, A.121, I.140, T.141, A.142 Ligands: NAD.3 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:T.117, C:G.118, C:F.119, C:F.120, C:T.141, C:T.141 EDO.5: 6 residues within 4Å: Chain C: Q.205, M.206, I.207 Chain D: Q.205, M.206, I.207 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:I.207, C:I.207

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ayres, C.A. et al., Structure of Streptococcus agalactiae glyceraldehyde-3-phosphate dehydrogenase holoenzyme reveals a novel surface. Acta Crystallogr F Struct Biol Commun (2014)

Release Date

2014-10-15

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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