SMTL ID : 2vhw.1

Crystal structure of holo L-alanine dehydrogenase from Mycobacterium tuberculosis in the open and closed conformation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-hexamer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: E.323, H.327 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.327, H2O.8, H2O.8, H2O.8 MG.3: 2 residues within 4Å: Chain B: D.326, H.327 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:H.327, H2O.9, H2O.19, H2O.20, H2O.20

6 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.2: 27 residues within 4Å: Chain A: L.130, M.133, S.134, A.137, I.174, G.175, G.177, T.178, A.179, L.197, D.198, I.199, K.203, S.220, A.238, V.239, L.240, V.241, L.249, I.267, D.270, Q.271, V.298, A.299, N.300, M.301, P.302 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:A.137, A:I.267 Hydrogen bonds: A:S.134, A:T.178, A:A.179, A:I.199, A:K.203, A:S.220, A:V.239, A:L.240, A:Q.271, A:V.298, A:M.301 Water bridges: A:G.177, A:T.178, A:G.180, A:K.203, A:K.203 Salt bridges: A:K.203 NAI.4: 26 residues within 4Å: Chain B: L.130, M.133, S.134, A.137, I.174, G.175, G.177, T.178, A.179, L.197, D.198, I.199, K.203, S.220, A.238, V.239, L.240, L.249, I.267, D.270, Q.271, V.298, A.299, N.300, M.301, P.302 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:A.137, B:I.267 Hydrogen bonds: B:S.134, B:T.178, B:T.178, B:T.178, B:A.179, B:I.199, B:S.220, B:V.239, B:L.240, B:I.267, B:M.301 Water bridges: B:G.177, B:T.178, B:G.180, B:K.203, B:S.220, B:S.220 NAI.5: 27 residues within 4Å: Chain C: M.133, S.134, A.137, I.174, G.175, G.177, T.178, A.179, L.197, D.198, I.199, K.203, S.220, A.238, V.239, L.240, V.241, L.249, I.267, A.268, I.269, D.270, V.298, A.299, N.300, M.301, P.302 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:A.137, C:I.267 Hydrogen bonds: C:S.134, C:T.178, C:T.178, C:A.179, C:I.199, C:K.203, C:K.203, C:S.220, C:V.239, C:L.240, C:V.298, C:M.301 Water bridges: C:S.134, C:G.177, C:T.178, C:G.180, C:S.220 Salt bridges: C:K.203 NAI.6: 26 residues within 4Å: Chain D: M.133, S.134, A.137, I.174, G.175, G.177, T.178, A.179, L.197, D.198, I.199, K.203, S.220, A.238, V.239, L.240, V.241, L.249, I.267, D.270, Q.271, V.298, A.299, N.300, M.301, P.302 21 PLIP interactions: 21 interactions with chain D Hydrophobic interactions: D:A.137, D:I.267 Hydrogen bonds: D:S.134, D:T.178, D:A.179, D:I.199, D:K.203, D:K.203, D:S.220, D:V.239, D:L.240, D:V.298, D:M.301 Water bridges: D:G.177, D:T.178, D:T.178, D:T.178, D:G.180, D:K.203, D:S.220 Salt bridges: D:K.203 NAI.7: 26 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 20 PLIP interactions: 20 interactions with chain E Hydrophobic interactions: E:M.133, E:A.137 Hydrogen bonds: E:S.134, E:T.178, 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:I.267, E:M.301 Water bridges: E:K.75, E:H.96, E:G.177, E:T.178, E:G.180 Salt bridges: E:K.203 NAI.8: 26 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, D.270, Q.271, V.298, A.299, N.300, M.301, P.302 21 PLIP interactions: 21 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:T.178, F:T.178, 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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