SMTL ID : 1uxp.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-tetramer

Ligands

4 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 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 Chain B: R.440 Chain C: Y.137, P.139, D.141, W.142, W.498 15 PLIP interactions: 11 interactions with chain A, 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: A:R.79, A:R.79, A:G.134, A:G.134, A:R.155, C:D.141, C:W.498 Water bridges: A:R.72, A:R.72, A:R.154, A:K.486, B:R.436 Salt bridges: A:R.72, A:R.154, B:R.440 AMP.4: 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 Chain D: Y.137, P.139, D.141, W.142, W.498 16 PLIP interactions: 12 interactions with chain B, 2 interactions with chain D, 2 interactions with chain A Hydrogen bonds: B:R.79, B:R.79, B:G.134, B:G.134, B:R.155, B:E.156, D:D.141, D:W.498 Water bridges: B:R.72, B:R.72, B:R.154, B:K.486, A:R.436 Salt bridges: B:R.72, B:R.154, A:R.440 AMP.7: 17 residues within 4Å: Chain A: Y.137, 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 Chain D: R.440 15 PLIP interactions: 11 interactions with chain C, 2 interactions with chain A, 2 interactions with chain D Hydrogen bonds: C:R.79, C:R.79, C:G.134, C:G.134, C:R.155, A:D.141, A:W.498 Water bridges: C:R.72, C:R.72, C:R.154, C:K.486, D:R.436 Salt bridges: C:R.72, C:R.154, D:R.440 AMP.10: 17 residues within 4Å: Chain B: Y.137, 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 16 PLIP interactions: 12 interactions with chain D, 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: D:R.79, D:R.79, D:G.134, D:G.134, D:R.155, D:E.156, B:D.141, B:W.498 Water bridges: D:R.72, D:R.72, D:R.154, D:K.486, C:R.436 Salt bridges: D:R.72, D:R.154, C:R.440

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

NAP.2: 32 residues within 4Å: Chain A: I.164, T.165, P.166, F.167, N.168, 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, V.251, E.263, L.264, G.265, G.266, C.297, E.395, F.397, L.423, H.455, F.462 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:T.242 Hydrogen bonds: A:T.165, A:T.165, A:F.167, A:I.194, A:G.224, A:E.228, 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, A:E.395, A:E.395 Salt bridges: A:K.191 NAP.5: 32 residues within 4Å: Chain B: I.164, T.165, P.166, F.167, N.168, 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, V.251, E.263, L.264, G.265, G.266, C.297, E.395, F.397, L.423, H.455, F.462 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:T.242 Hydrogen bonds: B:T.165, B:T.165, B:F.167, B:I.194, B:G.224, B:E.228, 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, B:E.395 Salt bridges: B:K.191 NAP.8: 32 residues within 4Å: Chain C: I.164, T.165, P.166, F.167, N.168, 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, V.251, E.263, L.264, G.265, G.266, C.297, E.395, F.397, L.423, H.455, F.462 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:T.242 Hydrogen bonds: C:T.165, C:T.165, C:F.167, C:I.194, C:G.224, C:E.228, 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, C:E.395, C:E.395 Salt bridges: C:K.191 NAP.11: 32 residues within 4Å: Chain D: I.164, T.165, P.166, F.167, N.168, 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, V.251, E.263, L.264, G.265, G.266, C.297, E.395, F.397, L.423, H.455, F.462 21 PLIP interactions: 21 interactions with chain D Hydrophobic interactions: D:T.242 Hydrogen bonds: D:T.165, D:T.165, D:F.167, D:I.194, D:G.224, D:E.228, 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, D:E.395 Salt bridges: D:K.191

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

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

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