SMTL ID : 5hko.1

Crystal structure of ABC transporter Solute Binding Protein MSMEG_3598 from Mycobacterium smegmatis str. MC2 155, target EFI-510969, in complex with L-sorbitol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

monomer

Ligands

15 x ZN: ZINC ION(Non-covalent)(Non-functional Binders)

ZN.1: 4 residues within 4Å: Chain A: E.49, E.251 Ligands: CL.16, CL.17 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.49, A:E.251 ZN.2: 3 residues within 4Å: Chain A: D.127 Ligands: CL.21, ACT.31 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.127, A:D.127 ZN.3: 3 residues within 4Å: Chain A: E.52 Ligands: IMD.27, ACT.32 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.52, A:E.52, H2O.7 ZN.4: 3 residues within 4Å: Chain A: N.156, D.217 Ligands: ACT.33 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.217, A:D.217, H2O.10, H2O.10 ZN.5: 1 residues within 4Å: Chain A: D.135 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.135, A:D.135, H2O.10, H2O.10 ZN.6: 3 residues within 4Å: Chain A: E.236 Ligands: IMD.29, IMD.30 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.236, A:E.236, H2O.9 ZN.7: 2 residues within 4Å: Chain A: D.336, T.346 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.336, A:D.336, H2O.7 ZN.8: 4 residues within 4Å: Chain A: K.51, D.55 Ligands: CL.18, CL.19 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.55 ZN.9: 2 residues within 4Å: Chain A: D.73, S.75 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.73, A:D.73, A:S.75, H2O.1, H2O.8 ZN.10: 1 residues within 4Å: Chain A: D.199 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.199 ZN.11: 2 residues within 4Å: Chain A: N.131, D.293 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.293, A:D.293, H2O.10, H2O.11 ZN.12: 2 residues within 4Å: Chain A: E.169 Ligands: CL.20 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.169, A:E.169, H2O.1, H2O.10 ZN.13: 4 residues within 4Å: Chain A: D.42, N.71 Ligands: CL.22, IMD.26 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.42, A:D.42 ZN.14: 3 residues within 4Å: Ligands: CL.23, CL.24, IMD.28 No protein-ligand interaction detected (PLIP) ZN.15: 1 residues within 4Å: Chain A: E.124 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.124, H2O.10

9 x CL: CHLORIDE ION(Non-functional Binders)

CL.16: 7 residues within 4Å: Chain A: E.49, R.198, I.250, E.251, D.252 Ligands: ZN.1, CL.17 Ligand excluded by PLIP CL.17: 6 residues within 4Å: Chain A: S.45, T.48, E.49, E.251 Ligands: ZN.1, CL.16 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain A: E.52, D.55 Ligands: ZN.8, CL.19 Ligand excluded by PLIP CL.19: 4 residues within 4Å: Chain A: D.55, K.59 Ligands: ZN.8, CL.18 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain A: Q.161, E.169 Ligands: ZN.12 Ligand excluded by PLIP CL.21: 4 residues within 4Å: Chain A: P.126, D.127 Ligands: ZN.2, ACT.31 Ligand excluded by PLIP CL.22: 6 residues within 4Å: Chain A: D.42, N.71, N.72, K.197 Ligands: ZN.13, IMD.26 Ligand excluded by PLIP CL.23: 3 residues within 4Å: Ligands: ZN.14, CL.24, IMD.28 Ligand excluded by PLIP CL.24: 3 residues within 4Å: Ligands: ZN.14, CL.23, IMD.28 Ligand excluded by PLIP

1 x 62W: L-glucitol(Non-covalent)

62W.25: 10 residues within 4Å: Chain A: Y.41, F.46, N.120, A.121, G.168, R.172, W.196, N.223, D.248, Q.268 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:Y.41, A:Y.41, A:N.120, A:G.168, A:R.172, A:R.172, A:N.223, A:Q.268, A:Q.268 Water bridges: A:P.96, A:P.96, A:V.97, A:N.120, A:D.224

5 x IMD: IMIDAZOLE(Non-covalent)

IMD.26: 4 residues within 4Å: Chain A: D.42, M.43 Ligands: ZN.13, CL.22 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.42 IMD.27: 5 residues within 4Å: Chain A: E.52, E.251, R.317 Ligands: ZN.3, ACT.32 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:R.317 IMD.28: 7 residues within 4Å: Chain A: Q.142, Q.145, M.146, A.300 Ligands: ZN.14, CL.23, CL.24 No protein-ligand interaction detected (PLIP) IMD.29: 4 residues within 4Å: Chain A: K.206, E.236 Ligands: ZN.6, IMD.30 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.206, A:E.236 IMD.30: 3 residues within 4Å: Chain A: E.236 Ligands: ZN.6, IMD.29 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.236, A:E.236

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.31: 4 residues within 4Å: Chain A: K.110, D.127 Ligands: ZN.2, CL.21 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.110 ACT.32: 5 residues within 4Å: Chain A: E.52, R.317, Q.318 Ligands: ZN.3, IMD.27 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.317, A:Q.318 Salt bridges: A:R.317 ACT.33: 4 residues within 4Å: Chain A: P.214, Q.215, D.217 Ligands: ZN.4 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.215 Water bridges: A:N.156

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Roth, Y. et al., Crystal structure of ABC transporter Solute Binding Protein MSMEG_3598 from Mycobacterium smegmatis str. MC2 155, target EFI-510969, in complex with L-sorbitol. To be published

Release Date

2016-02-03

Peptides

ABC transporter, carbohydrate uptake transporter-2 (CUT2) family, periplasmic sugar-binding protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

ABC transporter, carbohydrate uptake transporter-2 (CUT2) family, periplasmic sugar-binding protein