SMTL ID : 4lmp.2 (2 other biounits)

Mycobacterium tuberculosis L-alanine dehydrogenase x-ray structure in complex with N6-methyl adenosine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 x 6MD: N-methyladenosine(Non-covalent)

6MD.1: 13 residues within 4Å: Chain A: I.174, G.175, L.197, D.198, I.199, N.200, K.203, S.220, A.238, V.239, L.240, L.249 Ligands: GOL.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.199, A:K.203, A:S.220, A:L.240, A:L.240 6MD.9: 13 residues within 4Å: Chain B: I.174, G.175, L.197, D.198, I.199, N.200, K.203, S.220, A.238, V.239, L.240, L.249 Ligands: GOL.10 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:I.199, B:K.203, B:S.220, B:L.240, B:L.240

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: G.177, T.178, A.179 Ligands: 6MD.1, GOL.5 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.134, A:T.178, A:T.178, A:A.179 Water bridges: A:G.177, A:A.238 GOL.3: 8 residues within 4Å: Chain A: L.130, M.133, S.134, A.137, L.240, I.267, P.302 Ligands: SO4.8 No protein-ligand interaction detected (PLIP) GOL.4: 8 residues within 4Å: Chain A: A.116, T.119, K.341, G.342, L.343, S.344, S.352, V.355 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.343, A:S.352 GOL.5: 6 residues within 4Å: Chain A: A.126, L.127, A.131, S.134, T.178 Ligands: GOL.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.127, A:S.134, A:S.134 GOL.10: 5 residues within 4Å: Chain B: G.177, T.178, A.179 Ligands: 6MD.9, GOL.13 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.134, B:T.178, B:A.179 Water bridges: B:G.177, B:A.238 GOL.11: 8 residues within 4Å: Chain B: L.130, M.133, S.134, A.137, L.240, I.267, P.302 Ligands: SO4.16 No protein-ligand interaction detected (PLIP) GOL.12: 8 residues within 4Å: Chain B: A.116, T.119, K.341, G.342, L.343, S.344, S.352, V.355 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.119, B:L.343, B:S.352 GOL.13: 6 residues within 4Å: Chain B: A.126, L.127, A.131, S.134, T.178 Ligands: GOL.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.127, B:S.134, B:S.134

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 4 residues within 4Å: Chain A: R.156, E.167, K.259 Chain B: K.307 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Salt bridges: B:K.307, A:R.156, A:K.259 Water bridges: A:R.156 SO4.7: 4 residues within 4Å: Chain A: V.58, G.59, T.60, Q.63 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.59, A:T.60 SO4.8: 6 residues within 4Å: Chain A: R.15, K.75, M.133, N.300, P.302 Ligands: GOL.3 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.15, A:K.75 SO4.14: 4 residues within 4Å: Chain A: K.307 Chain B: R.156, E.167, K.259 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Water bridges: B:R.156 Salt bridges: B:R.156, B:K.259, A:K.307 SO4.15: 4 residues within 4Å: Chain B: V.58, G.59, T.60, Q.63 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.59, B:T.60 SO4.16: 6 residues within 4Å: Chain B: R.15, K.75, M.133, N.300, P.302 Ligands: GOL.11 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.15, B:K.75

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, H.-B. et al., Drug target analysis by dye-ligand affinity chromatography. To be Published

Release Date

2013-11-06

Peptides

Alanine dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Alanine dehydrogenase

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