SMTL ID : 3gpd.1

TWINNING IN CRYSTALS OF HUMAN SKELETAL MUSCLE D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

homo-tetramer

Ligands

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 5 residues within 4Å: Chain A: T.181, A.182, T.183, R.233 Ligands: NAD.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.182, A:T.183, A:R.233 SO4.2: 5 residues within 4Å: Chain A: S.150, C.151, T.152, T.210, G.211 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.150, A:T.153, A:T.153, A:G.211 SO4.4: 3 residues within 4Å: Chain B: T.181, T.183 Ligands: NAD.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.183, B:T.183 SO4.5: 6 residues within 4Å: Chain B: S.150, C.151, T.152, T.153, T.210, G.211 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.150, B:T.152, B:T.152, B:T.153, B:T.153, B:G.211 SO4.7: 5 residues within 4Å: Chain C: T.181, A.182, T.183, R.233 Ligands: NAD.9 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:A.182, C:T.183, C:R.233 SO4.8: 5 residues within 4Å: Chain C: S.150, C.151, T.152, T.210, G.211 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.150, C:T.153, C:G.211 SO4.10: 3 residues within 4Å: Chain D: T.181, T.183 Ligands: NAD.12 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.181, D:T.183, D:T.183 SO4.11: 6 residues within 4Å: Chain D: S.150, C.151, T.152, T.153, T.210, G.211 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:S.150, D:T.152, D:T.152, D:T.152, D:T.153, D:T.153, D:G.211

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

NAD.3: 23 residues within 4Å: Chain A: D.8, G.9, G.11, R.12, I.13, N.33, D.34, P.35, F.36, E.78, R.79, D.80, S.97, T.98, S.121, A.122, C.151, I.180, T.181, A.182, N.315, E.316 Ligands: SO4.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.8, A:I.13, A:N.33, A:D.80, A:S.97, A:T.98, A:A.182 NAD.6: 22 residues within 4Å: Chain B: D.8, G.9, G.11, R.12, I.13, D.34, P.35, E.78, R.79, D.80, S.97, T.98, G.99, F.101, S.121, A.122, C.151, T.181, A.182, N.315, E.316 Ligands: SO4.4 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.13, B:N.315 Hydrogen bonds: B:D.8, B:I.13, B:N.33, B:E.78, B:D.80 pi-Stacking: B:P.35 NAD.9: 23 residues within 4Å: Chain C: D.8, G.9, G.11, R.12, I.13, N.33, D.34, P.35, F.36, E.78, R.79, D.80, S.97, T.98, S.121, A.122, C.151, I.180, T.181, A.182, N.315, E.316 Ligands: SO4.7 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:D.8, C:I.13, C:N.33, C:D.80, C:S.97, C:T.98, C:A.182 NAD.12: 22 residues within 4Å: Chain D: D.8, G.9, G.11, R.12, I.13, D.34, P.35, E.78, R.79, D.80, S.97, T.98, G.99, F.101, S.121, A.122, C.151, T.181, A.182, N.315, E.316 Ligands: SO4.10 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:I.13, D:N.315 Hydrogen bonds: D:D.8, D:I.13, D:N.33, D:E.78, D:D.80 pi-Stacking: D:P.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mercer, W.D. et al., Twinning in crystals of human skeletal muscle D-glyceraldehyde-3-phosphate dehydrogenase. J.Mol.Biol. (1976)

Release Date

1983-10-27

Peptides

D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
R

B
G

C
R

D
G

D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE