SMTL ID : 5xlv.1

Mycobacterium tuberculosis Pantothenate kinase mutant F254A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 8 residues within 4Å: Chain A: S.98, V.99, A.100, V.101, G.102, K.103, S.104, R.238 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:A.100, A:V.101, A:G.102, A:K.103, A:S.104 Water bridges: A:G.102, A:K.103, A:K.103, A:T.105 Salt bridges: A:K.103, A:R.238 SO4.2: 3 residues within 4Å: Chain A: P.85, D.86, R.87 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.86, A:D.86, A:D.86, A:R.87 Water bridges: A:R.87, A:R.87 Salt bridges: A:R.87 SO4.25: 8 residues within 4Å: Chain B: S.98, V.99, A.100, V.101, G.102, K.103, S.104, R.238 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:A.100, B:V.101, B:G.102, B:K.103, B:S.104 Water bridges: B:K.103, B:K.103, B:T.105 Salt bridges: B:K.103, B:R.238 SO4.26: 3 residues within 4Å: Chain B: P.85, D.86, R.87 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.86, B:D.86, B:R.87, B:G.168 Water bridges: B:R.87 Salt bridges: B:R.87

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.3: 7 residues within 4Å: Chain A: L.132, K.147, Y.177, Y.182, I.272, I.276, N.277 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.177 Water bridges: A:Y.235, A:Y.235, A:Y.235, A:Y.235 PG4.27: 10 residues within 4Å: Chain B: D.129, L.132, K.147, Y.177, H.179, Y.182, Y.235, F.239, I.272, N.277 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.179, B:Y.235 Water bridges: B:Y.177, B:N.277

38 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 7 residues within 4Å: Chain A: Q.43, I.44, D.45, E.48, Y.53, T.105, T.106 Ligand excluded by PLIP EDO.5: 3 residues within 4Å: Chain A: R.289, R.306, R.308 Ligand excluded by PLIP EDO.6: 4 residues within 4Å: Chain A: R.227, I.228, E.229, L.286 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: L.138, Q.139, N.142, L.143, M.144, H.145 Ligand excluded by PLIP EDO.8: 3 residues within 4Å: Chain A: E.12, R.297, R.306 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: D.14, R.15, R.16, N.305 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain A: Y.133, P.134, N.154 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain A: G.41, E.42 Ligands: GOL.23 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain A: P.250, E.251, S.252, H.253 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain A: A.259, F.260, S.261 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain A: Y.257, F.260 Ligands: EDO.19, EDO.20 Ligand excluded by PLIP EDO.15: 7 residues within 4Å: Chain A: R.67, V.89, K.166, D.219 Chain B: R.310, K.311, L.312 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain A: P.134, I.184, P.186, G.187 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain A: L.180, T.245, A.246, A.248, D.249 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain A: R.146, P.150, E.151, N.284 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain A: F.260, Q.264 Ligands: EDO.14 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain A: V.267, A.268, E.271 Ligands: EDO.14 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain A: S.215, D.216, F.218, R.291 Chain B: D.216 Ligand excluded by PLIP EDO.22: 2 residues within 4Å: Chain A: R.16, Q.17 Ligand excluded by PLIP EDO.28: 3 residues within 4Å: Chain B: Y.133, R.141, R.156 Ligand excluded by PLIP EDO.29: 2 residues within 4Å: Chain B: R.116, W.117 Ligand excluded by PLIP EDO.30: 4 residues within 4Å: Chain B: N.154, R.156, R.160 Ligands: GOL.47 Ligand excluded by PLIP EDO.31: 3 residues within 4Å: Chain B: R.306, R.308 Ligands: EDO.43 Ligand excluded by PLIP EDO.32: 4 residues within 4Å: Chain B: S.237, L.240, A.241 Ligands: EDO.35 Ligand excluded by PLIP EDO.33: 3 residues within 4Å: Chain B: S.237, R.238, A.241 Ligand excluded by PLIP EDO.34: 4 residues within 4Å: Chain B: Q.233, W.234, S.237, H.302 Ligand excluded by PLIP EDO.35: 5 residues within 4Å: Chain B: Q.233, V.236, S.237, L.240 Ligands: EDO.32 Ligand excluded by PLIP EDO.36: 4 residues within 4Å: Chain B: A.226, R.227, I.228, L.286 Ligand excluded by PLIP EDO.37: 4 residues within 4Å: Chain B: F.71, A.75, E.80, D.86 Ligand excluded by PLIP EDO.38: 4 residues within 4Å: Chain B: F.131, C.173, A.174, P.175 Ligand excluded by PLIP EDO.39: 2 residues within 4Å: Chain B: R.278, V.282 Ligand excluded by PLIP EDO.40: 4 residues within 4Å: Chain B: Y.10, R.289, P.290, R.308 Ligand excluded by PLIP EDO.41: 4 residues within 4Å: Chain B: S.104, L.125, T.127, Q.190 Ligand excluded by PLIP EDO.42: 3 residues within 4Å: Chain B: R.141, L.143, E.151 Ligand excluded by PLIP EDO.43: 3 residues within 4Å: Chain B: R.297, R.306 Ligands: EDO.31 Ligand excluded by PLIP EDO.44: 3 residues within 4Å: Chain B: E.76, G.79, E.80 Ligand excluded by PLIP EDO.45: 4 residues within 4Å: Chain B: D.14, R.15, R.16, N.305 Ligand excluded by PLIP EDO.46: 3 residues within 4Å: Chain B: S.169, D.170, Y.171 Ligand excluded by PLIP

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.23: 4 residues within 4Å: Chain A: S.104, R.108, H.179 Ligands: EDO.11 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.104, A:R.108 Water bridges: A:S.104, A:T.127, A:H.179, A:E.201 GOL.24: 1 residues within 4Å: Chain A: E.42 No protein-ligand interaction detected (PLIP) GOL.47: 6 residues within 4Å: Chain B: Y.133, P.134, E.137, R.141, N.154 Ligands: EDO.30 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.137, B:R.141, B:N.154 Water bridges: B:E.137, B:R.140

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Paul, A. et al., Biochemical and structural studies of mutants indicate concerted movement of the dimer interface and ligand-binding region of Mycobacterium tuberculosis pantothenate kinase. Acta Crystallogr F Struct Biol Commun (2017)

Release Date

2018-05-16

Peptides

Pantothenate kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Pantothenate kinase