SMTL ID : 3pym.1

Structure of GAPDH 3 from S.cerevisiae at 2.0 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 21 residues within 4Å: Chain A: N.7, G.8, F.9, G.10, R.11, I.12, N.32, D.33, P.34, F.35, R.78, S.96, T.97, G.98, F.100, T.120, A.121, C.150, A.181, N.314, Y.318 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.12, A:Y.318 Hydrogen bonds: A:N.7, A:F.9, A:R.11, A:I.12, A:R.78, A:N.314 Water bridges: A:G.10, A:G.13, A:N.32, A:E.315, A:E.315 pi-Stacking: A:F.35 NAD.3: 21 residues within 4Å: Chain B: N.7, G.8, F.9, G.10, R.11, I.12, N.32, D.33, P.34, F.35, R.78, S.96, T.97, G.98, T.120, A.121, C.150, A.181, N.314, Y.318 Chain C: P.189 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:I.12, B:Y.318 Hydrogen bonds: B:F.9, B:F.9, B:G.10, B:R.11, B:I.12, B:N.32, B:R.78, B:N.314 Water bridges: B:N.7, B:G.13, B:E.315, B:E.315 NAD.6: 21 residues within 4Å: Chain C: N.7, G.8, F.9, G.10, R.11, I.12, N.32, D.33, P.34, F.35, R.78, S.96, T.97, G.98, F.100, T.120, A.121, C.150, A.181, N.314, Y.318 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:I.12, C:Y.318 Hydrogen bonds: C:N.7, C:F.9, C:R.11, C:I.12, C:R.78, C:T.120, C:N.314 Water bridges: C:G.10, C:G.13, C:N.32, C:E.315 pi-Stacking: C:F.35 NAD.8: 21 residues within 4Å: Chain A: P.189 Chain D: N.7, G.8, F.9, G.10, R.11, I.12, N.32, D.33, P.34, F.35, R.78, S.96, T.97, G.98, T.120, A.121, C.150, A.181, N.314, Y.318 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:I.12, D:Y.318 Hydrogen bonds: D:F.9, D:F.9, D:G.10, D:R.11, D:I.12, D:N.32, D:R.78, D:T.120, D:N.314 Water bridges: D:N.7, D:G.13, D:E.315

4 x MRY: MESO-ERYTHRITOL(Non-covalent)

MRY.2: 9 residues within 4Å: Chain A: A.42, Y.43, K.46, Y.47, V.58, S.59, H.60 Chain B: D.277 Chain D: W.194 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:V.58, A:H.60 Water bridges: A:Y.43, A:V.58, B:D.277 MRY.4: 5 residues within 4Å: Chain A: D.277 Chain B: A.42, Y.43, K.46, V.58 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:D.277, B:V.58 Water bridges: A:D.277, B:Y.43, B:Y.43, B:V.58 MRY.7: 9 residues within 4Å: Chain B: W.194 Chain C: A.42, Y.43, K.46, Y.47, V.58, S.59, H.60 Chain D: D.277 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:V.58, C:H.60 Water bridges: C:Y.43, C:V.58, D:D.277 MRY.9: 5 residues within 4Å: Chain C: D.277 Chain D: A.42, Y.43, K.46, V.58 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:D.277, D:V.58 Water bridges: C:D.277, C:D.277, D:Y.43, D:Y.43, D:V.58

2 x NA: SODIUM ION(Non-functional Binders)

NA.5: 4 residues within 4Å: Chain B: A.20, L.21, R.23, V.26 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.21, B:R.23 NA.10: 4 residues within 4Å: Chain D: A.20, L.21, R.23, V.26 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:L.21, D:R.23

Links

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Citation

 - 

Release Date

2012-01-11

Peptides

Glyceraldehyde-3-phosphate dehydrogenase 3: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Glyceraldehyde-3-phosphate dehydrogenase 3