SMTL ID : 4rs3.1

Crystal structure of carbohydrate transporter A0QYB3 from Mycobacterium smegmatis str. MC2 155, target EFI-510969, in complex with xylitol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

1 x XYL: Xylitol(Non-covalent)

XYL.1: 10 residues within 4Å: Chain A: Y.20, F.25, N.99, A.100, G.147, R.151, W.175, N.202, D.227, Q.247 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:Y.20, A:Y.20, A:N.99, A:G.147, A:R.151, A:R.151, A:N.202, A:Q.247 Water bridges: A:N.99, A:D.203, A:D.227

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

ZN.2: 3 residues within 4Å: Chain A: D.128 Ligands: IMD.13, CL.19 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.128 ZN.3: 4 residues within 4Å: Chain A: E.31 Ligands: IMD.14, CL.23, CL.28 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.31, A:E.31 ZN.4: 4 residues within 4Å: Chain A: K.30, D.34 Ligands: CL.20, CL.21 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.34 ZN.5: 4 residues within 4Å: Chain A: E.28, E.230 Ligands: CL.17, CL.18 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.28, A:E.230 ZN.6: 3 residues within 4Å: Chain A: E.215 Ligands: IMD.16, ACT.34 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.215, A:E.215, H2O.9 ZN.7: 4 residues within 4Å: Chain A: D.178 Ligands: CL.29, CL.30, CL.32 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.178 ZN.8: 2 residues within 4Å: Chain A: D.315, T.325 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.315, A:D.315, H2O.8 ZN.9: 1 residues within 4Å: Chain A: D.114 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.114, A:D.114, H2O.7, H2O.7, H2O.9 ZN.10: 4 residues within 4Å: Chain A: D.156, K.170 Ligands: CL.22, ACT.33 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.156 ZN.11: 5 residues within 4Å: Chain A: N.135, D.196 Ligands: CL.24, CL.25, ACT.36 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.196, A:D.196 ZN.12: 3 residues within 4Å: Ligands: IMD.15, CL.27, CL.31 No protein-ligand interaction detected (PLIP)

4 x IMD: IMIDAZOLE(Non-covalent)

IMD.13: 6 residues within 4Å: Chain A: Q.124, D.128 Ligands: ZN.2, IMD.15, CL.19, CL.27 No protein-ligand interaction detected (PLIP) IMD.14: 5 residues within 4Å: Chain A: E.31, E.230, R.296 Ligands: ZN.3, CL.28 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:R.296 IMD.15: 9 residues within 4Å: Chain A: Q.121, Q.124, M.125 Ligands: ZN.12, IMD.13, CL.19, CL.26, CL.27, CL.31 No protein-ligand interaction detected (PLIP) IMD.16: 3 residues within 4Å: Chain A: E.215 Ligands: ZN.6, ACT.34 No protein-ligand interaction detected (PLIP)

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

CL.17: 6 residues within 4Å: Chain A: E.28, I.229, E.230, D.231 Ligands: ZN.5, CL.18 Ligand excluded by PLIP CL.18: 5 residues within 4Å: Chain A: S.24, E.28, E.230 Ligands: ZN.5, CL.17 Ligand excluded by PLIP CL.19: 4 residues within 4Å: Chain A: D.128 Ligands: ZN.2, IMD.13, IMD.15 Ligand excluded by PLIP CL.20: 5 residues within 4Å: Chain A: D.34, K.38 Ligands: ZN.4, CL.21, ACT.35 Ligand excluded by PLIP CL.21: 4 residues within 4Å: Chain A: E.31, D.34 Ligands: ZN.4, CL.20 Ligand excluded by PLIP CL.22: 6 residues within 4Å: Chain A: I.138, D.156, L.159, V.167 Ligands: ZN.10, ACT.33 Ligand excluded by PLIP CL.23: 4 residues within 4Å: Chain A: E.31, Q.297 Ligands: ZN.3, CL.28 Ligand excluded by PLIP CL.24: 4 residues within 4Å: Chain A: D.196 Ligands: ZN.11, CL.25, ACT.36 Ligand excluded by PLIP CL.25: 7 residues within 4Å: Chain A: K.133, G.134, N.135, D.196 Ligands: ZN.11, CL.24, ACT.36 Ligand excluded by PLIP CL.26: 3 residues within 4Å: Chain A: Q.121 Ligands: IMD.15, CL.27 Ligand excluded by PLIP CL.27: 5 residues within 4Å: Ligands: ZN.12, IMD.13, IMD.15, CL.26, CL.31 Ligand excluded by PLIP CL.28: 4 residues within 4Å: Chain A: E.31 Ligands: ZN.3, IMD.14, CL.23 Ligand excluded by PLIP CL.29: 2 residues within 4Å: Chain A: D.178 Ligands: ZN.7 Ligand excluded by PLIP CL.30: 2 residues within 4Å: Chain A: D.178 Ligands: ZN.7 Ligand excluded by PLIP CL.31: 3 residues within 4Å: Ligands: ZN.12, IMD.15, CL.27 Ligand excluded by PLIP CL.32: 4 residues within 4Å: Chain A: D.178, V.181, Q.211 Ligands: ZN.7 Ligand excluded by PLIP

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

ACT.33: 7 residues within 4Å: Chain A: Q.140, G.152, I.155, D.156, K.170 Ligands: ZN.10, CL.22 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.155 Hydrogen bonds: A:Q.140, A:D.156 Salt bridges: A:K.170 ACT.34: 4 residues within 4Å: Chain A: K.185, E.215 Ligands: ZN.6, IMD.16 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.185 ACT.35: 6 residues within 4Å: Chain A: D.34, K.38, I.42, E.43, L.44 Ligands: CL.20 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.38 Hydrogen bonds: A:D.34, A:L.44 Water bridges: A:K.30 ACT.36: 7 residues within 4Å: Chain A: N.135, P.193, Q.194, D.196 Ligands: ZN.11, CL.24, CL.25 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.135 Water bridges: A:D.196

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, H. et al., A General Strategy for the Discovery of Metabolic Pathways: d-Threitol, l-Threitol, and Erythritol Utilization in Mycobacterium smegmatis. J.Am.Chem.Soc. (2015)

Release Date

2014-11-19

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