SMTL ID : 1uxu.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 2.25 Å

Oligo State

homo-tetramer

Ligands

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

NAP.1: 24 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, G.243, S.244, V.247, R.250, V.251, G.265, E.395, F.397 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:T.165, A:F.167, A:K.191, A:I.194, A:L.222, A:G.224, A:E.228, A:S.244, A:E.395 Water bridges: A:S.193, A:R.250 Salt bridges: A:K.191 NAP.5: 24 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, G.243, S.244, V.247, R.250, V.251, G.265, E.395, F.397 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:T.165, B:F.167, B:K.191, B:I.194, B:L.222, B:G.224, B:E.228, B:E.228, B:S.244, B:E.395 Water bridges: B:S.193, B:R.250 Salt bridges: B:K.191 NAP.9: 24 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, G.243, S.244, V.247, R.250, V.251, G.265, E.395, F.397 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:T.165, C:F.167, C:K.191, C:I.194, C:L.222, C:G.224, C:E.228, C:S.244, C:E.395 Water bridges: C:S.193, C:R.250 Salt bridges: C:K.191 NAP.13: 24 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, G.243, S.244, V.247, R.250, V.251, G.265, E.395, F.397 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:T.165, D:F.167, D:K.191, D:I.194, D:L.222, D:G.224, D:E.228, D:E.228, D:S.244, D:E.395 Water bridges: D:S.193, D:R.250 Salt bridges: D:K.191

4 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.2: 14 residues within 4Å: Chain A: R.72, R.79, I.133, G.134, G.135, R.154, R.155, E.156, Y.184 Chain B: R.440 Chain C: P.139, D.141, W.142, W.498 15 PLIP interactions: 11 interactions with chain A, 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: A:R.79, A:R.79, A:G.134, A:R.155, A:E.156, A:E.156, C:D.141 Water bridges: A:R.72, A:R.154, A:R.154, C:E.501, B:R.436 Salt bridges: A:R.72, A:R.154, B:R.440 AMP.6: 14 residues within 4Å: Chain A: R.440 Chain B: R.72, R.79, I.133, G.134, G.135, R.154, R.155, E.156, Y.184 Chain D: P.139, D.141, W.142, W.498 14 PLIP interactions: 10 interactions with chain B, 2 interactions with chain A, 2 interactions with chain D Hydrogen bonds: B:R.79, B:R.79, B:G.134, B:R.155, B:E.156, D:D.141 Water bridges: B:R.72, B:R.154, B:R.154, A:R.436, D:E.501 Salt bridges: B:R.72, B:R.154, A:R.440 AMP.10: 14 residues within 4Å: Chain A: P.139, D.141, W.142, W.498 Chain C: R.72, R.79, I.133, G.134, G.135, R.154, R.155, E.156, Y.184 Chain D: R.440 15 PLIP interactions: 2 interactions with chain D, 11 interactions with chain C, 2 interactions with chain A Water bridges: D:R.436, C:R.72, C:R.154, C:R.154, A:E.501 Salt bridges: D:R.440, C:R.72, C:R.154 Hydrogen bonds: C:R.79, C:R.79, C:G.134, C:R.155, C:E.156, C:E.156, A:D.141 AMP.14: 14 residues within 4Å: Chain B: P.139, D.141, W.142, W.498 Chain C: R.440 Chain D: R.72, R.79, I.133, G.134, G.135, R.154, R.155, E.156, Y.184 14 PLIP interactions: 9 interactions with chain D, 2 interactions with chain C, 3 interactions with chain B Hydrogen bonds: D:R.79, D:R.79, D:G.134, D:R.155, D:E.156, B:D.141 Water bridges: D:R.154, D:R.154, C:R.436, B:E.501, B:E.501 Salt bridges: D:R.72, D:R.154, C:R.440

4 x G3H: GLYCERALDEHYDE-3-PHOSPHATE(Non-covalent)

G3H.3: 8 residues within 4Å: Chain A: N.168, Y.169, R.296, C.297, D.298, R.454, H.455, G.456 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:N.168, A:C.297, A:D.298, A:H.455, A:H.455, A:G.456 Water bridges: A:R.296, A:R.296, A:G.456 Salt bridges: A:R.296 G3H.7: 8 residues within 4Å: Chain B: N.168, Y.169, R.296, C.297, D.298, R.454, H.455, G.456 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:N.168, B:C.297, B:D.298, B:H.455, B:G.456 Water bridges: B:R.296, B:R.296, B:G.456 Salt bridges: B:R.296 G3H.11: 8 residues within 4Å: Chain C: N.168, Y.169, R.296, C.297, D.298, R.454, H.455, G.456 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:N.168, C:C.297, C:D.298, C:H.455, C:H.455, C:G.456 Water bridges: C:R.296, C:R.296, C:G.456 Salt bridges: C:R.296 G3H.15: 8 residues within 4Å: Chain D: N.168, Y.169, R.296, C.297, D.298, R.454, H.455, G.456 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:N.168, D:C.297, D:D.298, D:H.455, D:G.456 Water bridges: D:R.296, D:R.296, D:G.456 Salt bridges: D:R.296

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

NA.4: 3 residues within 4Å: Chain A: G.255, G.256 Chain B: E.249 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.255 NA.8: 3 residues within 4Å: Chain A: E.249 Chain B: G.255, G.256 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:D.234, A:E.249 Hydrogen bonds: A:E.249 NA.12: 3 residues within 4Å: Chain C: G.255, G.256 Chain D: E.249 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.249 NA.16: 3 residues within 4Å: Chain C: E.249 Chain D: G.255, G.256 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Water bridges: D:D.234, C:E.249 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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