SMTL ID : 1uxv.1

Structural basis for allosteric regulation and substrate specificity of the non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPN) from Thermoproteus tenax

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-tetramer

Ligands

4 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 32 residues within 4Å: Chain A: I.164, T.165, P.166, F.167, N.168, Y.169, K.191, P.192, S.193, I.194, L.222, P.223, G.224, K.225, A.227, E.228, F.241, T.242, G.243, S.244, V.247, R.250, E.263, L.264, G.265, G.266, C.297, E.395, F.397, L.423, H.455, F.462 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:Y.169, A:T.242 Hydrogen bonds: A:T.165, A:F.167, A:I.194, A:L.222, A:G.224, A:E.228, A:S.244, A:E.263, A:G.265, A:G.266, A:E.395, A:H.455 Water bridges: A:S.193, A:S.195, A:S.195, A:T.245 Salt bridges: A:K.191 NAP.4: 32 residues within 4Å: Chain B: I.164, T.165, P.166, F.167, N.168, Y.169, K.191, P.192, S.193, I.194, L.222, P.223, G.224, K.225, A.227, E.228, F.241, T.242, G.243, S.244, V.247, R.250, E.263, L.264, G.265, G.266, C.297, E.395, F.397, L.423, H.455, F.462 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:Y.169, B:T.242 Hydrogen bonds: B:T.165, B:F.167, B:I.194, B:L.222, B:G.224, B:E.228, B:E.228, B:S.244, B:E.263, B:E.263, B:G.265, B:G.266, B:E.395 Water bridges: B:S.193, B:S.195, B:S.195, B:T.245 Salt bridges: B:K.191 NAP.7: 32 residues within 4Å: Chain C: I.164, T.165, P.166, F.167, N.168, Y.169, K.191, P.192, S.193, I.194, L.222, P.223, G.224, K.225, A.227, E.228, F.241, T.242, G.243, S.244, V.247, R.250, E.263, L.264, G.265, G.266, C.297, E.395, F.397, L.423, H.455, F.462 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:Y.169, C:T.242 Hydrogen bonds: C:T.165, C:F.167, C:I.194, C:L.222, C:G.224, C:E.228, C:S.244, C:E.263, C:G.265, C:G.266, C:E.395, C:H.455 Water bridges: C:S.193, C:S.195, C:S.195, C:T.245 Salt bridges: C:K.191 NAP.10: 32 residues within 4Å: Chain D: I.164, T.165, P.166, F.167, N.168, Y.169, K.191, P.192, S.193, I.194, L.222, P.223, G.224, K.225, A.227, E.228, F.241, T.242, G.243, S.244, V.247, R.250, E.263, L.264, G.265, G.266, C.297, E.395, F.397, L.423, H.455, F.462 20 PLIP interactions: 20 interactions with chain D Hydrophobic interactions: D:Y.169, D:T.242 Hydrogen bonds: D:T.165, D:F.167, D:I.194, D:L.222, D:G.224, D:E.228, D:E.228, D:S.244, D:E.263, D:E.263, D:G.265, D:G.266, D:E.395 Water bridges: D:S.193, D:S.195, D:S.195, D:T.245 Salt bridges: D:K.191

4 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.2: 17 residues within 4Å: Chain A: R.72, R.79, K.132, I.133, G.134, G.135, R.154, R.155, E.156, P.157, Y.184, V.479 Chain B: R.440 Chain C: P.139, D.141, W.142, W.498 14 PLIP interactions: 7 interactions with chain A, 2 interactions with chain C, 5 interactions with chain B Hydrogen bonds: A:R.79, A:K.132, A:G.134, A:R.155, A:E.156, C:D.141, C:W.498 Salt bridges: A:R.72, A:R.154, B:R.440 Water bridges: B:R.436, B:R.436, B:R.440, B:R.440 AMP.5: 17 residues within 4Å: Chain A: R.440 Chain B: R.72, R.79, K.132, I.133, G.134, G.135, R.154, R.155, E.156, P.157, Y.184, V.479 Chain D: P.139, D.141, W.142, W.498 13 PLIP interactions: 6 interactions with chain B, 5 interactions with chain A, 2 interactions with chain D Hydrogen bonds: B:R.79, B:K.132, B:G.134, B:R.155, D:D.141, D:W.498 Salt bridges: B:R.72, B:R.154, A:R.440 Water bridges: A:R.436, A:R.436, A:R.440, A:R.440 AMP.8: 17 residues within 4Å: Chain A: P.139, D.141, W.142, W.498 Chain C: R.72, R.79, K.132, I.133, G.134, G.135, R.154, R.155, E.156, P.157, Y.184, V.479 Chain D: R.440 14 PLIP interactions: 7 interactions with chain C, 5 interactions with chain D, 2 interactions with chain A Hydrogen bonds: C:R.79, C:K.132, C:G.134, C:R.155, C:E.156, A:D.141, A:W.498 Salt bridges: C:R.72, C:R.154, D:R.440 Water bridges: D:R.436, D:R.436, D:R.440, D:R.440 AMP.11: 17 residues within 4Å: Chain B: P.139, D.141, W.142, W.498 Chain C: R.440 Chain D: R.72, R.79, K.132, I.133, G.134, G.135, R.154, R.155, E.156, P.157, Y.184, V.479 13 PLIP interactions: 6 interactions with chain D, 5 interactions with chain C, 2 interactions with chain B Hydrogen bonds: D:R.79, D:K.132, D:G.134, D:R.155, B:D.141, B:W.498 Salt bridges: D:R.72, D:R.154, C:R.440 Water bridges: C:R.436, C:R.436, C:R.440, C:R.440

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

NA.3: 4 residues within 4Å: Chain A: D.234, G.255, G.256 Chain B: E.249 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.249 Water bridges: B:K.253, B:K.253, A:V.257 NA.6: 4 residues within 4Å: Chain A: E.249 Chain B: D.234, G.255, G.256 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.255 Water bridges: B:D.234, B:V.257, A:E.249, A:K.253 NA.9: 4 residues within 4Å: Chain C: D.234, G.255, G.256 Chain D: E.249 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:E.249 Water bridges: D:K.253, D:K.253, C:V.257 NA.12: 4 residues within 4Å: Chain C: E.249 Chain D: D.234, G.255, G.256 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain C Water bridges: D:D.234, D:V.257, C:E.249, C:K.253 Hydrogen bonds: C:E.249

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lorentzen, E. et al., Structural Basis of Allosteric Regulation and Substrate Specificity of the Non-Phosphorylating Glyceraldehyde 3-Phosphate Dehydrogenase from Thermoproteus Tenax. J.Mol.Biol. (2004)

Release Date

2004-08-05

Peptides

GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE (NADP+): ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE (NADP+)