SMTL ID : 4lmp.3 (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-hexamer

Ligands

6 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 6MD.17: 13 residues within 4Å: Chain C: 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.18 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:I.199, C:K.203, C:S.220, C:L.240, C:L.240 6MD.25: 13 residues within 4Å: Chain D: 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.26 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:I.199, D:K.203, D:S.220, D:L.240, D:L.240 6MD.33: 13 residues within 4Å: Chain E: 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.34 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:I.199, E:K.203, E:S.220, E:L.240, E:L.240 6MD.41: 13 residues within 4Å: Chain F: 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.42 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:I.199, F:K.203, F:S.220, F:L.240, F:L.240

24 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 Ligand excluded by PLIP 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 Ligand excluded by 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 Ligand excluded by PLIP GOL.5: 6 residues within 4Å: Chain A: A.126, L.127, A.131, S.134, T.178 Ligands: GOL.2 Ligand excluded by PLIP GOL.10: 5 residues within 4Å: Chain B: G.177, T.178, A.179 Ligands: 6MD.9, GOL.13 Ligand excluded by PLIP 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 Ligand excluded by 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 Ligand excluded by PLIP GOL.13: 6 residues within 4Å: Chain B: A.126, L.127, A.131, S.134, T.178 Ligands: GOL.10 Ligand excluded by PLIP GOL.18: 5 residues within 4Å: Chain C: G.177, T.178, A.179 Ligands: 6MD.17, GOL.21 Ligand excluded by PLIP GOL.19: 8 residues within 4Å: Chain C: L.130, M.133, S.134, A.137, L.240, I.267, P.302 Ligands: SO4.24 Ligand excluded by PLIP GOL.20: 8 residues within 4Å: Chain C: A.116, T.119, K.341, G.342, L.343, S.344, S.352, V.355 Ligand excluded by PLIP GOL.21: 6 residues within 4Å: Chain C: A.126, L.127, A.131, S.134, T.178 Ligands: GOL.18 Ligand excluded by PLIP GOL.26: 5 residues within 4Å: Chain D: G.177, T.178, A.179 Ligands: 6MD.25, GOL.29 Ligand excluded by PLIP GOL.27: 8 residues within 4Å: Chain D: L.130, M.133, S.134, A.137, L.240, I.267, P.302 Ligands: SO4.32 Ligand excluded by PLIP GOL.28: 8 residues within 4Å: Chain D: A.116, T.119, K.341, G.342, L.343, S.344, S.352, V.355 Ligand excluded by PLIP GOL.29: 6 residues within 4Å: Chain D: A.126, L.127, A.131, S.134, T.178 Ligands: GOL.26 Ligand excluded by PLIP GOL.34: 5 residues within 4Å: Chain E: G.177, T.178, A.179 Ligands: 6MD.33, GOL.37 Ligand excluded by PLIP GOL.35: 8 residues within 4Å: Chain E: L.130, M.133, S.134, A.137, L.240, I.267, P.302 Ligands: SO4.40 Ligand excluded by PLIP GOL.36: 8 residues within 4Å: Chain E: A.116, T.119, K.341, G.342, L.343, S.344, S.352, V.355 Ligand excluded by PLIP GOL.37: 6 residues within 4Å: Chain E: A.126, L.127, A.131, S.134, T.178 Ligands: GOL.34 Ligand excluded by PLIP GOL.42: 5 residues within 4Å: Chain F: G.177, T.178, A.179 Ligands: 6MD.41, GOL.45 Ligand excluded by PLIP GOL.43: 8 residues within 4Å: Chain F: L.130, M.133, S.134, A.137, L.240, I.267, P.302 Ligands: SO4.48 Ligand excluded by PLIP GOL.44: 8 residues within 4Å: Chain F: A.116, T.119, K.341, G.342, L.343, S.344, S.352, V.355 Ligand excluded by PLIP GOL.45: 6 residues within 4Å: Chain F: A.126, L.127, A.131, S.134, T.178 Ligands: GOL.42 Ligand excluded by PLIP

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

SO4.6: 4 residues within 4Å: Chain A: R.156, E.167, K.259 Chain F: K.307 Ligand excluded by PLIP SO4.7: 4 residues within 4Å: Chain A: V.58, G.59, T.60, Q.63 Ligand excluded by PLIP SO4.8: 6 residues within 4Å: Chain A: R.15, K.75, M.133, N.300, P.302 Ligands: GOL.3 Ligand excluded by PLIP SO4.14: 4 residues within 4Å: Chain B: R.156, E.167, K.259 Chain E: K.307 Ligand excluded by PLIP SO4.15: 4 residues within 4Å: Chain B: V.58, G.59, T.60, Q.63 Ligand excluded by PLIP SO4.16: 6 residues within 4Å: Chain B: R.15, K.75, M.133, N.300, P.302 Ligands: GOL.11 Ligand excluded by PLIP SO4.22: 4 residues within 4Å: Chain C: R.156, E.167, K.259 Chain D: K.307 Ligand excluded by PLIP SO4.23: 4 residues within 4Å: Chain C: V.58, G.59, T.60, Q.63 Ligand excluded by PLIP SO4.24: 6 residues within 4Å: Chain C: R.15, K.75, M.133, N.300, P.302 Ligands: GOL.19 Ligand excluded by PLIP SO4.30: 4 residues within 4Å: Chain C: K.307 Chain D: R.156, E.167, K.259 Ligand excluded by PLIP SO4.31: 4 residues within 4Å: Chain D: V.58, G.59, T.60, Q.63 Ligand excluded by PLIP SO4.32: 6 residues within 4Å: Chain D: R.15, K.75, M.133, N.300, P.302 Ligands: GOL.27 Ligand excluded by PLIP SO4.38: 4 residues within 4Å: Chain B: K.307 Chain E: R.156, E.167, K.259 Ligand excluded by PLIP SO4.39: 4 residues within 4Å: Chain E: V.58, G.59, T.60, Q.63 Ligand excluded by PLIP SO4.40: 6 residues within 4Å: Chain E: R.15, K.75, M.133, N.300, P.302 Ligands: GOL.35 Ligand excluded by PLIP SO4.46: 4 residues within 4Å: Chain A: K.307 Chain F: R.156, E.167, K.259 Ligand excluded by PLIP SO4.47: 4 residues within 4Å: Chain F: V.58, G.59, T.60, Q.63 Ligand excluded by PLIP SO4.48: 6 residues within 4Å: Chain F: R.15, K.75, M.133, N.300, P.302 Ligands: GOL.43 Ligand excluded by PLIP

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: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Alanine dehydrogenase

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