SMTL ID : 2vhx.1

Crystal structure of the ternary complex of L-alanine dehydrogenase from Mycobacterium tuberculosis with NAD+ and pyruvate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-hexamer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: E.323, H.327 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.327 MG.3: 2 residues within 4Å: Chain B: D.326, H.327 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.327 MG.9: 2 residues within 4Å: Chain F: E.323, H.327 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:H.327

6 x PYR: PYRUVIC ACID(Non-covalent)

PYR.2: 9 residues within 4Å: Chain A: R.15, K.75, F.94, H.96, L.130, M.133, D.270, N.300, P.302 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.15, A:K.75 PYR.4: 7 residues within 4Å: Chain B: R.15, K.75, F.94, H.96, L.130, M.133, N.300 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.94, B:L.130 Hydrogen bonds: B:K.75, B:N.300 Salt bridges: B:R.15, B:K.75 PYR.5: 6 residues within 4Å: Chain C: R.15, K.75, H.96, L.130, M.133, N.300 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.130 Hydrogen bonds: C:K.75, C:N.300 Salt bridges: C:R.15, C:K.75 PYR.6: 8 residues within 4Å: Chain D: R.15, K.75, F.94, H.96, L.130, M.133, N.300, P.302 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:F.94, D:L.130 Hydrogen bonds: D:K.75, D:N.300 Salt bridges: D:R.15, D:K.75 PYR.7: 11 residues within 4Å: Chain E: R.15, K.75, F.94, H.96, L.130, M.133, D.270, A.299, N.300, P.302 Ligands: NAD.8 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:L.130, E:M.133 Salt bridges: E:R.15, E:K.75 PYR.10: 11 residues within 4Å: Chain F: R.15, K.75, F.94, H.96, L.130, M.133, D.270, A.299, N.300, P.302 Ligands: NAD.11 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:L.130, F:M.133 Hydrogen bonds: F:K.75, F:D.270 Salt bridges: F:R.15, F:K.75

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

NAD.8: 27 residues within 4Å: Chain E: L.130, M.133, S.134, A.137, G.175, G.177, T.178, A.179, D.198, I.199, N.200, K.203, S.220, A.238, V.239, L.240, L.249, I.267, A.268, D.270, Q.271, V.298, A.299, N.300, M.301, P.302 Ligands: PYR.7 20 PLIP interactions: 20 interactions with chain E Hydrophobic interactions: E:M.133, E:A.137 Hydrogen bonds: E:S.134, E:G.177, E:T.178, E:A.179, E:I.199, E:K.203, E:K.203, E:S.220, E:V.239, E:L.240, E:V.298, E:M.301 Water bridges: E:H.96, E:T.178, E:G.180, E:K.203, E:D.270 Salt bridges: E:K.203 NAD.11: 28 residues within 4Å: Chain F: L.130, M.133, S.134, A.137, G.175, G.177, T.178, A.179, D.198, I.199, N.200, K.203, S.220, A.238, V.239, L.240, L.249, I.267, A.268, I.269, D.270, Q.271, V.298, A.299, N.300, M.301, P.302 Ligands: PYR.10 19 PLIP interactions: 19 interactions with chain F Hydrophobic interactions: F:M.133, F:A.137 Hydrogen bonds: F:S.134, F:T.178, F:T.178, F:A.179, F:I.199, F:K.203, F:S.220, F:V.239, F:L.240, F:I.267, F:M.301 Water bridges: F:H.96, F:G.177, F:G.180, F:K.203, F:K.203 Salt bridges: F:K.203

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Agren, D. et al., Three-Dimensional Structures of Apo- and Holo-L-Alanine Dehydrogenase from Mycobacterium Tuberculosis Reveal Conformational Changes Upon Coenzyme Binding. J.Mol.Biol. (2008)

Release Date

2008-03-11

Peptides

ALANINE DEHYDROGENASE: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

ALANINE DEHYDROGENASE

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