SMTL ID : 2voj.1

Ternary complex of M. tuberculosis Rv2780 with NAD and pyruvate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-hexamer

Ligands

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

NAD.1: 25 residues within 4Å: Chain A: L.130, M.133, S.134, A.137, G.175, A.176, G.177, T.178, A.179, D.198, I.199, K.203, S.220, A.238, V.239, L.240, L.249, I.267, A.268, D.270, Q.271, N.300, M.301, P.302 Ligands: 2OP.2 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:L.130, A:A.137 Hydrogen bonds: A:S.134, A:T.178, A:T.178, A:A.179, A:I.199, A:K.203, A:K.203, A:S.220, A:V.239, A:L.240, A:D.270, A:D.270, A:N.300, A:M.301 Water bridges: A:G.177, A:G.180, A:K.203 Salt bridges: A:K.203 NAD.3: 24 residues within 4Å: Chain B: L.130, M.133, S.134, A.137, I.174, G.175, G.177, T.178, A.179, D.198, I.199, K.203, S.220, A.238, V.239, L.240, L.249, I.267, A.268, D.270, N.300, M.301, P.302 Ligands: 2OP.4 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:L.130, B:A.137 Hydrogen bonds: B:S.134, B:T.178, B:A.179, B:I.199, B:K.203, B:K.203, B:S.220, B:V.239, B:L.240, B:D.270, B:N.300, B:M.301 Water bridges: B:H.96, B:G.177, B:T.178, B:G.180, B:K.203, B:Q.271 Salt bridges: B:K.203 NAD.5: 25 residues within 4Å: Chain C: 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, N.300, M.301, P.302 Ligands: 2OP.6 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:L.130, C:A.137 Hydrogen bonds: C:S.134, C:T.178, C:A.179, C:I.199, C:K.203, C:S.220, C:V.239, C:L.240, C:D.270, C:N.300, C:M.301 Water bridges: C:G.177, C:G.180 Salt bridges: C:K.203 NAD.7: 25 residues within 4Å: Chain D: L.130, M.133, S.134, A.137, G.175, A.176, G.177, T.178, A.179, D.198, I.199, K.203, S.220, A.238, V.239, L.240, L.249, I.267, A.268, D.270, Q.271, N.300, M.301, P.302 Ligands: 2OP.8 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:L.130, D:A.137 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:D.270, D:N.300, D:M.301 Water bridges: D:G.177, D:T.178, D:G.180, D:K.203 Salt bridges: D:K.203 NAD.9: 24 residues within 4Å: Chain E: L.130, M.133, S.134, A.137, I.174, G.175, G.177, T.178, A.179, D.198, I.199, K.203, S.220, A.238, V.239, L.240, L.249, I.267, A.268, D.270, N.300, M.301, P.302 Ligands: 2OP.10 22 PLIP interactions: 22 interactions with chain E Hydrophobic interactions: E:L.130, 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:D.270, E:D.270, E:N.300, E:M.301 Water bridges: E:H.96, E:G.177, E:G.180, E:K.203, E:Q.271 Salt bridges: E:K.203 NAD.11: 25 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, N.300, M.301, P.302 Ligands: 2OP.12 18 PLIP interactions: 18 interactions with chain F Hydrophobic interactions: F:L.130, 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:D.270, F:D.270, F:N.300, F:M.301 Water bridges: F:G.177, F:G.180 Salt bridges: F:K.203

6 x 2OP: (2S)-2-HYDROXYPROPANOIC ACID(Non-covalent)

2OP.2: 10 residues within 4Å: Chain A: R.15, K.75, F.94, H.96, L.130, M.133, D.270, N.300, P.302 Ligands: NAD.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.94, A:L.130 Hydrogen bonds: A:K.75, A:D.270 Water bridges: A:H.96 Salt bridges: A:R.15, A:K.75 2OP.4: 10 residues within 4Å: Chain B: R.15, K.75, F.94, H.96, L.130, M.133, D.270, N.300, P.302 Ligands: NAD.3 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.94, B:L.130 Hydrogen bonds: B:K.75, B:K.75, B:N.300 Water bridges: B:H.96 Salt bridges: B:R.15, B:K.75 2OP.6: 10 residues within 4Å: Chain C: R.15, K.75, F.94, H.96, L.130, M.133, D.270, N.300, P.302 Ligands: NAD.5 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.94, C:L.130 Hydrogen bonds: C:K.75, C:K.75 Salt bridges: C:R.15, C:K.75 2OP.8: 10 residues within 4Å: Chain D: R.15, K.75, F.94, H.96, L.130, M.133, D.270, N.300, P.302 Ligands: NAD.7 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:F.94, D:L.130 Hydrogen bonds: D:K.75 Salt bridges: D:R.15, D:K.75 2OP.10: 10 residues within 4Å: Chain E: R.15, K.75, F.94, H.96, L.130, M.133, D.270, N.300, P.302 Ligands: NAD.9 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:F.94, E:L.130 Hydrogen bonds: E:K.75, E:K.75, E:D.270, E:N.300 Salt bridges: E:R.15, E:K.75 2OP.12: 10 residues within 4Å: Chain F: R.15, K.75, F.94, H.96, L.130, M.133, D.270, N.300, P.302 Ligands: NAD.11 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:F.94, F:L.130 Hydrogen bonds: F:K.75, F:K.75, F:D.270 Water bridges: F:H.96 Salt bridges: F:R.15, F:K.75

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tripathi, S.M. et al., Crystal Structures of the Mycobacterium Tuberculosis Secretory Antigen Alanine Dehydrogenase (Rv2780) in Apo and Ternary Complex Forms Captures "Open" and "Closed" Enzyme Conformations. Proteins: Struct., Funct., Bioinf. (2008)

Release Date

2008-03-04

Peptides

ALANINE DEHYDROGENASE: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
E

D
A

E
C

F
E

ALANINE DEHYDROGENASE

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