SMTL ID : 8hyh.1

Structure of amino acid dehydrogenase3448

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

homo-hexamer

Ligands

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

NAD.1: 21 residues within 4Å: Chain A: R.124, T.125, L.126, L.129, T.130, S.133, G.174, G.175, G.176, V.177, V.178, I.196, D.197, L.198, N.199, S.219, A.237, V.238, L.239, I.240, L.248 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:L.126, A:L.126, A:S.133, A:S.133, A:V.177, A:V.178, A:L.198, A:S.219, A:S.219, A:A.237, A:L.239 Water bridges: A:G.176, A:G.179, A:I.240, A:I.240 NAD.5: 21 residues within 4Å: Chain B: R.124, T.125, L.126, L.129, T.130, S.133, G.174, G.175, G.176, V.177, V.178, I.196, D.197, L.198, N.199, S.219, A.237, V.238, L.239, I.240, L.248 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:L.126, B:L.126, B:S.133, B:S.133, B:V.177, B:V.178, B:L.198, B:S.219, B:S.219, B:A.237, B:L.239 Water bridges: B:G.176, B:G.179, B:I.240, B:I.240 NAD.9: 21 residues within 4Å: Chain C: R.124, T.125, L.126, L.129, T.130, S.133, G.174, G.175, G.176, V.177, V.178, I.196, D.197, L.198, N.199, S.219, A.237, V.238, L.239, I.240, L.248 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:L.126, C:L.126, C:S.133, C:S.133, C:V.177, C:V.178, C:L.198, C:S.219, C:S.219, C:A.237, C:L.239 Water bridges: C:G.176, C:G.179, C:I.240, C:I.240 NAD.13: 21 residues within 4Å: Chain D: R.124, T.125, L.126, L.129, T.130, S.133, G.174, G.175, G.176, V.177, V.178, I.196, D.197, L.198, N.199, S.219, A.237, V.238, L.239, I.240, L.248 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:L.126, D:L.126, D:S.133, D:S.133, D:V.177, D:V.178, D:L.198, D:S.219, D:S.219, D:A.237, D:L.239 Water bridges: D:G.176, D:G.179, D:I.240, D:I.240 NAD.17: 21 residues within 4Å: Chain E: R.124, T.125, L.126, L.129, T.130, S.133, G.174, G.175, G.176, V.177, V.178, I.196, D.197, L.198, N.199, S.219, A.237, V.238, L.239, I.240, L.248 15 PLIP interactions: 15 interactions with chain E Hydrogen bonds: E:L.126, E:L.126, E:S.133, E:S.133, E:V.177, E:V.178, E:L.198, E:S.219, E:S.219, E:A.237, E:L.239 Water bridges: E:G.176, E:G.179, E:I.240, E:I.240 NAD.21: 21 residues within 4Å: Chain F: R.124, T.125, L.126, L.129, T.130, S.133, G.174, G.175, G.176, V.177, V.178, I.196, D.197, L.198, N.199, S.219, A.237, V.238, L.239, I.240, L.248 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:L.126, F:L.126, F:S.133, F:S.133, F:V.177, F:V.178, F:L.198, F:S.219, F:S.219, F:A.237, F:L.239 Water bridges: F:G.176, F:G.179, F:I.240, F:I.240

12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 5 residues within 4Å: Chain A: V.187, G.190, A.191, Q.213 Chain F: N.212 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain F Hydrogen bonds: A:V.187, A:G.190 Water bridges: F:N.212 EDO.3: 9 residues within 4Å: Chain A: G.160, G.161, V.162, V.165, R.167 Chain F: D.207, I.214, T.215, T.216 6 PLIP interactions: 3 interactions with chain F, 2 interactions with chain A, 1 interactions with chain E Hydrogen bonds: F:D.207, F:D.207, F:T.216, A:V.165, A:R.167 Water bridges: E:R.138 EDO.6: 5 residues within 4Å: Chain B: V.187, G.190, A.191, Q.213 Chain E: N.212 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain B Water bridges: E:N.212 Hydrogen bonds: B:V.187, B:G.190 EDO.7: 9 residues within 4Å: Chain B: G.160, G.161, V.162, V.165, R.167 Chain E: D.207, I.214, T.215, T.216 6 PLIP interactions: 2 interactions with chain B, 3 interactions with chain E, 1 interactions with chain D Hydrogen bonds: B:V.165, B:R.167, E:D.207, E:D.207, E:T.216 Water bridges: D:R.138 EDO.10: 5 residues within 4Å: Chain C: V.187, G.190, A.191, Q.213 Chain D: N.212 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:V.187, C:G.190 Water bridges: D:N.212 EDO.11: 9 residues within 4Å: Chain C: G.160, G.161, V.162, V.165, R.167 Chain D: D.207, I.214, T.215, T.216 6 PLIP interactions: 3 interactions with chain D, 1 interactions with chain F, 2 interactions with chain C Hydrogen bonds: D:D.207, D:D.207, D:T.216, C:V.165, C:R.167 Water bridges: F:R.138 EDO.14: 5 residues within 4Å: Chain C: N.212 Chain D: V.187, G.190, A.191, Q.213 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Water bridges: C:N.212 Hydrogen bonds: D:V.187, D:G.190 EDO.15: 9 residues within 4Å: Chain C: D.207, I.214, T.215, T.216 Chain D: G.160, G.161, V.162, V.165, R.167 5 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: D:V.165, D:R.167, C:D.207, C:T.216 Water bridges: B:R.138 EDO.18: 5 residues within 4Å: Chain B: N.212 Chain E: V.187, G.190, A.191, Q.213 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain B Hydrogen bonds: E:V.187, E:G.190 Water bridges: B:N.212 EDO.19: 9 residues within 4Å: Chain B: D.207, I.214, T.215, T.216 Chain E: G.160, G.161, V.162, V.165, R.167 5 PLIP interactions: 2 interactions with chain E, 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: E:V.165, E:R.167, B:D.207, B:T.216 Water bridges: A:R.138 EDO.22: 5 residues within 4Å: Chain A: N.212 Chain F: V.187, G.190, A.191, Q.213 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain F Water bridges: A:N.212 Hydrogen bonds: F:V.187, F:G.190 EDO.23: 9 residues within 4Å: Chain A: D.207, I.214, T.215, T.216 Chain F: G.160, G.161, V.162, V.165, R.167 5 PLIP interactions: 2 interactions with chain F, 1 interactions with chain C, 2 interactions with chain A Hydrogen bonds: F:V.165, F:R.167, A:D.207, A:T.216 Water bridges: C:R.138

6 x PYR: PYRUVIC ACID(Non-covalent)

PYR.4: 7 residues within 4Å: Chain A: R.15, K.75, Y.94, H.96, L.129, M.132, N.300 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.129 Hydrogen bonds: A:K.75, A:N.300 Salt bridges: A:R.15, A:K.75 PYR.8: 7 residues within 4Å: Chain B: R.15, K.75, Y.94, H.96, L.129, M.132, N.300 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.129 Hydrogen bonds: B:K.75, B:N.300 Salt bridges: B:R.15, B:K.75 PYR.12: 7 residues within 4Å: Chain C: R.15, K.75, Y.94, H.96, L.129, M.132, N.300 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.129 Hydrogen bonds: C:K.75, C:N.300 Salt bridges: C:R.15, C:K.75 PYR.16: 7 residues within 4Å: Chain D: R.15, K.75, Y.94, H.96, L.129, M.132, N.300 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:L.129 Hydrogen bonds: D:K.75, D:N.300 Salt bridges: D:R.15, D:K.75 PYR.20: 7 residues within 4Å: Chain E: R.15, K.75, Y.94, H.96, L.129, M.132, N.300 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:L.129 Hydrogen bonds: E:K.75, E:N.300 Salt bridges: E:R.15, E:K.75 PYR.24: 7 residues within 4Å: Chain F: R.15, K.75, Y.94, H.96, L.129, M.132, N.300 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:L.129 Hydrogen bonds: F:K.75, F:N.300 Salt bridges: F:R.15, F:K.75

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maeno, M. et al., Two different alanine dehydrogenases from Geobacillus kaustophilus: Their biochemical characteristics and differential expression in vegetative cells and spores. Biochim Biophys Acta Proteins Proteom (2023)

Release Date

2023-04-05

Peptides

Alanine dehydrogenase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Alanine dehydrogenase