SMTL ID : 8hye.1

Structure of amino acid dehydrogenase-2752 with ligand

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-hexamer

Ligands

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

NAD.1: 23 residues within 4Å: Chain A: L.129, M.132, S.133, A.136, I.173, G.174, G.175, G.176, T.177, A.178, L.196, D.197, I.198, N.199, S.219, V.238, L.239, L.248, V.266, A.267, Q.270, N.300, P.302 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:L.129, A:M.132 Hydrogen bonds: A:S.133, A:T.177, A:A.178, A:G.179, A:I.198, A:S.219, A:S.219, A:V.238, A:N.300 Water bridges: A:G.176, A:G.176, A:N.199, A:N.300, A:N.300, A:M.301 NAD.4: 23 residues within 4Å: Chain B: L.129, M.132, S.133, A.136, G.174, G.175, G.176, T.177, A.178, G.179, D.197, I.198, N.199, S.219, A.237, V.238, L.239, L.248, V.266, A.267, Q.270, N.300, P.302 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:L.129, B:M.132 Hydrogen bonds: B:S.133, B:G.176, B:G.176, B:T.177, B:T.177, B:A.178, B:G.179, B:I.198, B:S.219, B:V.238, B:N.300 Water bridges: B:S.219, B:M.301 NAD.5: 23 residues within 4Å: Chain C: M.132, S.133, A.136, G.174, G.175, G.176, T.177, A.178, L.196, D.197, I.198, S.219, A.237, V.238, L.239, L.248, V.266, A.267, D.269, Q.270, N.300, M.301, P.302 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:M.132, C:A.136 Hydrogen bonds: C:S.133, C:G.175, C:G.176, C:T.177, C:T.177, C:A.178, C:I.198, C:S.219, C:S.219, C:V.238, C:L.239, C:Q.270, C:N.300, C:M.301 Water bridges: C:N.199 NAD.8: 23 residues within 4Å: Chain D: L.129, M.132, S.133, A.136, I.173, G.174, G.175, G.176, T.177, A.178, L.196, D.197, I.198, N.199, S.219, V.238, L.239, L.248, V.266, A.267, Q.270, N.300, P.302 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:L.129, D:M.132 Hydrogen bonds: D:S.133, D:T.177, D:T.177, D:A.178, D:G.179, D:I.198, D:S.219, D:S.219, D:V.238, D:N.300 Water bridges: D:G.176, D:G.176, D:N.199, D:N.300, D:N.300, D:M.301 NAD.11: 23 residues within 4Å: Chain E: L.129, M.132, S.133, A.136, G.174, G.175, G.176, T.177, A.178, G.179, D.197, I.198, N.199, S.219, A.237, V.238, L.239, L.248, V.266, A.267, Q.270, N.300, P.302 14 PLIP interactions: 14 interactions with chain E Hydrophobic interactions: E:L.129, E:M.132 Hydrogen bonds: E:S.133, E:G.176, E:G.176, E:T.177, E:A.178, E:G.179, E:I.198, E:S.219, E:V.238, E:N.300 Water bridges: E:S.219, E:M.301 NAD.12: 23 residues within 4Å: Chain F: M.132, S.133, A.136, G.174, G.175, G.176, T.177, A.178, L.196, D.197, I.198, S.219, A.237, V.238, L.239, L.248, V.266, A.267, D.269, Q.270, N.300, M.301, P.302 17 PLIP interactions: 17 interactions with chain F Hydrophobic interactions: F:M.132, F:A.136 Hydrogen bonds: F:S.133, F:G.175, F:G.176, F:T.177, F:A.178, F:I.198, F:S.219, F:S.219, F:V.238, F:L.239, F:Q.270, F:N.300, F:M.301 Water bridges: F:T.177, F:N.199

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

EDO.2: 2 residues within 4Å: Chain A: A.122, N.123 No protein-ligand interaction detected (PLIP) EDO.7: 3 residues within 4Å: Chain C: E.205, D.208, L.209 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.208, C:D.208, C:L.209 EDO.9: 2 residues within 4Å: Chain D: A.122, N.123 No protein-ligand interaction detected (PLIP) EDO.14: 3 residues within 4Å: Chain F: E.205, D.208, L.209 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:D.208, F:L.209

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.3: 13 residues within 4Å: Chain A: R.167, G.190, A.191, D.192, V.193, T.194, D.212, V.214, T.215 Chain E: R.167, D.192, D.212, Q.213 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:G.190, A:V.193, A:V.193, A:T.194, A:T.215, A:T.215, A:T.215 Water bridges: A:A.191, A:V.193 Salt bridges: A:D.192, E:D.192 EPE.10: 13 residues within 4Å: Chain B: R.167, D.192, D.212, Q.213 Chain D: R.167, G.190, A.191, D.192, V.193, T.194, D.212, V.214, T.215 12 PLIP interactions: 10 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:G.190, D:D.192, D:V.193, D:V.193, D:T.215, D:T.215, D:T.215 Water bridges: D:A.191, D:V.193, B:D.192 Salt bridges: D:D.192, B:D.192

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.6: 7 residues within 4Å: Chain C: Q.146, H.283, P.286, Y.296 Chain E: E.149, P.151, H.152 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain E Hydrogen bonds: C:Q.146, C:Y.296, E:E.149, E:E.149 Salt bridges: C:H.283, E:H.152 PO4.13: 7 residues within 4Å: Chain B: E.149, P.151, H.152 Chain F: Q.146, H.283, P.286, Y.296 6 PLIP interactions: 4 interactions with chain F, 2 interactions with chain B Hydrogen bonds: F:Q.146, F:Y.296, F:Y.296, B:E.149 Salt bridges: F:H.283, B:H.152

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
B

C
C

D
A

E
B

F
C

Alanine dehydrogenase