SMTL ID : 5utm.1

Mutant Structures of Streptococcus Agalactiae GBS Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 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 C: P.211 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:I.33, A:Y.340 Hydrogen bonds: A:F.30, A:F.30, A:R.32, A:I.33, A:R.98, A:N.336 Water bridges: A:N.28, A:N.28, A:G.31, A:G.34, A:G.118, A:T.141, A:G.203, A:G.203, A:G.203, A:G.203 NAD.3: 22 residues within 4Å: 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, N.336, Y.340 Chain D: P.211 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:I.33, B:Y.340 Hydrogen bonds: B:F.30, B:F.30, B:R.32, B:I.33, B:R.98, B:N.336 Water bridges: B:N.28, B:G.31, B:G.34, B:N.53, B:G.118, B:T.141, B:G.203, B:G.203, B:G.203, B:G.203 NAD.5: 22 residues within 4Å: Chain A: P.211 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, N.336, Y.340 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:I.33, C:Y.340 Hydrogen bonds: C:F.30, C:F.30, C:R.32, C:I.33, C:R.98, C:T.141, C:N.336 Water bridges: C:N.28, C:G.31, C:G.34, C:N.53, C:R.98, C:R.98, C:G.118, C:T.141, C:G.203, C:G.203, C:G.203, C:G.203 NAD.7: 22 residues within 4Å: Chain B: 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, N.336, Y.340 20 PLIP interactions: 20 interactions with chain D Hydrophobic interactions: D:I.33, D:Y.340 Hydrogen bonds: D:G.29, D:F.30, D:F.30, D:R.32, D:I.33, D:R.98, D:T.141, D:N.336 Water bridges: D:N.28, D:N.28, D:G.31, D:G.34, D:G.118, D:T.141, D:G.203, D:G.203, D:G.203, D:G.203

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: I.41, V.44, V.47 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:I.41, A:V.44, A:V.47, H2O.7, H2O.9 MG.4: 3 residues within 4Å: Chain B: I.41, V.44, V.47 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:I.41, B:V.44, B:V.47, H2O.17, H2O.18 MG.6: 3 residues within 4Å: Chain C: I.41, V.44, V.47 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:I.41, C:V.44, C:V.47, H2O.25 MG.8: 3 residues within 4Å: Chain D: I.41, V.44, V.47 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:I.41, D:V.44, D:V.47

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schormann, N. et al., Mutant Structures of Streptococcus agalactiae GAPDH. To Be Published

Release Date

2018-02-28

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