SMTL ID : 6c9n.1

Mycobacterium tuberculosis adenosine kinase bound to sangivamycin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

4 x SGV: SANGIVAMYCIN(Non-covalent)

SGV.1: 19 residues within 4Å: Chain A: S.8, A.10, D.12, G.47, G.48, V.49, N.52, F.102, F.116, M.121, A.146, Q.172, Q.173, T.253, G.254, D.257, T.293 Chain B: S.36, L.38 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Q.172 Hydrogen bonds: A:S.8, A:D.12, A:G.48, A:N.52, A:Q.172, A:Q.173, B:S.36, B:S.36 Water bridges: A:G.254, A:G.254, A:G.254 pi-Stacking: A:F.116, A:F.116 SGV.2: 9 residues within 4Å: Chain A: G.225, P.226, V.243, V.244, E.246, Q.249, V.255, V.285, L.288 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.288 Hydrogen bonds: A:E.246 Water bridges: A:G.228 SGV.6: 18 residues within 4Å: Chain A: S.36 Chain B: S.8, A.10, D.12, G.47, G.48, V.49, N.52, F.102, F.116, M.121, A.146, Q.172, Q.173, T.253, G.254, D.257, T.293 13 PLIP interactions: 2 interactions with chain A, 11 interactions with chain B Hydrogen bonds: A:S.36, A:S.36, B:D.12, B:G.48, B:N.52, B:Q.172, B:Q.173 Hydrophobic interactions: B:Q.172 Water bridges: B:G.254, B:G.254, B:D.257 pi-Stacking: B:F.116, B:F.116 SGV.7: 11 residues within 4Å: Chain B: G.225, P.226, V.243, V.244, P.245, E.246, Q.249, V.255, A.284, V.285, L.288 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.288 Hydrogen bonds: B:V.244, B:E.246 Water bridges: B:G.225, B:G.228, B:V.244

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 14 residues within 4Å: Chain A: M.15, T.103, C.104, T.105, I.113, A.114, S.115 Chain B: M.15, T.103, C.104, T.105, I.113, A.114, S.115 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:T.103, A:T.105, A:T.105, A:S.115, B:T.105, B:T.105, B:I.113

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

SO4.4: 6 residues within 4Å: Chain A: S.171, N.195, T.223, V.255, G.256, R.260 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.195, A:T.223, A:G.256 Water bridges: A:N.195, A:T.223, A:T.223, A:P.252, A:G.254, A:G.254 SO4.8: 5 residues within 4Å: Chain B: N.195, T.223, V.255, G.256, R.260 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.195, B:G.256 Water bridges: B:N.195, B:T.223, B:G.254, B:G.254, B:D.257

2 x NA: SODIUM ION(Non-functional Binders)

NA.5: 7 residues within 4Å: Chain A: D.251, T.253, V.287, S.290, T.291, G.292, T.293 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.251, A:D.251 NA.9: 7 residues within 4Å: Chain B: D.251, T.253, V.287, S.290, T.291, G.292, T.293 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.291

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Crespo, R.A. et al., Structure-Guided Drug Design of 6-Substituted Adenosine Analogues as Potent Inhibitors of Mycobacterium tuberculosis Adenosine Kinase. J.Med.Chem. (2019)

Release Date

2019-05-01

Peptides

Adenosine kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Adenosine kinase

Related Entries With Identical Sequence