SMTL ID : 6hyh.1

Crystal structure of MSMEG_1712 from Mycobacterium smegmatis in complex with Beta-D-Fucofuranose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

26 x ZN: ZINC ION(Non-covalent)

ZN.1: 1 residues within 4Å: Chain A: H.243 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.243, H2O.1, H2O.1, H2O.1 ZN.2: 3 residues within 4Å: Chain A: E.259, E.290 Chain B: H.314 5 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:H.314, A:E.259, A:E.259, A:E.290, H2O.1 ZN.3: 3 residues within 4Å: Chain A: D.87, D.111 Chain D: H.318 5 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: A:D.87, A:D.87, A:D.111, D:H.318, H2O.1 ZN.4: 2 residues within 4Å: Chain A: D.157, D.161 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.157, A:D.161 ZN.5: 4 residues within 4Å: Chain A: H.316, H.318 Chain B: H.316 Ligands: ZN.11 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.316, A:H.318, H2O.1, H2O.1 ZN.6: 1 residues within 4Å: Chain A: E.36 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.36, H2O.1 ZN.7: 3 residues within 4Å: Chain A: E.267, H.315, H.317 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.315, A:H.317, H2O.1 ZN.8: 3 residues within 4Å: Chain A: H.317, H.319 Chain B: E.125 5 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:H.317, A:H.319, B:E.125, B:E.125, H2O.1 ZN.10: 4 residues within 4Å: Chain A: H.314 Chain B: E.259, E.290, A.311 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:E.259, B:E.259, B:E.290, A:H.314, H2O.1 ZN.11: 4 residues within 4Å: Chain A: H.316 Chain B: H.316, H.318 Ligands: ZN.5 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.316, B:H.318, H2O.1, H2O.2 ZN.12: 3 residues within 4Å: Chain A: E.125 Chain B: H.317, H.319 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:H.317, B:H.319, A:E.125, A:E.125, H2O.1 ZN.13: 3 residues within 4Å: Chain B: E.267, H.315, H.317 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.315, B:H.317, H2O.1 ZN.14: 1 residues within 4Å: Chain B: H.243 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.243, H2O.1 ZN.16: 1 residues within 4Å: Chain C: H.243 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:H.243, H2O.2, H2O.2, H2O.2 ZN.17: 3 residues within 4Å: Chain C: E.259, E.290 Chain D: H.314 5 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: C:E.259, C:E.259, C:E.290, D:H.314, H2O.2 ZN.18: 3 residues within 4Å: Chain B: H.318 Chain C: D.87, D.111 5 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: B:H.318, C:D.87, C:D.87, C:D.111, H2O.2 ZN.19: 2 residues within 4Å: Chain C: D.157, D.161 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.157, C:D.161 ZN.20: 4 residues within 4Å: Chain C: H.316, H.318 Chain D: H.316 Ligands: ZN.26 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.316, C:H.318, H2O.2, H2O.2 ZN.21: 1 residues within 4Å: Chain C: E.36 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.36, H2O.2 ZN.22: 3 residues within 4Å: Chain C: E.267, H.315, H.317 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.315, C:H.317, H2O.2 ZN.23: 3 residues within 4Å: Chain C: H.317, H.319 Chain D: E.125 5 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: D:E.125, D:E.125, C:H.317, C:H.319, H2O.2 ZN.25: 4 residues within 4Å: Chain C: H.314 Chain D: E.259, E.290, A.311 5 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: D:E.259, D:E.259, D:E.290, C:H.314, H2O.2 ZN.26: 4 residues within 4Å: Chain C: H.316 Chain D: H.316, H.318 Ligands: ZN.20 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.316, D:H.318, H2O.2, H2O.3 ZN.27: 3 residues within 4Å: Chain C: E.125 Chain D: H.317, H.319 5 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: D:H.317, D:H.319, C:E.125, C:E.125, H2O.3 ZN.28: 3 residues within 4Å: Chain D: E.267, H.315, H.317 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.315, D:H.317, H2O.2 ZN.29: 1 residues within 4Å: Chain D: H.243 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.243, H2O.2

4 x GYE: beta-D-fucofuranose(Non-covalent)

GYE.9: 13 residues within 4Å: Chain A: E.27, S.28, W.30, R.31, D.104, R.105, F.123, P.158, R.162, F.186, N.212, D.240, C.260 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.123, A:P.158 Hydrogen bonds: A:S.28, A:S.28, A:R.31, A:D.104, A:R.105, A:R.162, A:R.162, A:N.212, A:D.240, A:D.240 Salt bridges: A:R.31, A:R.105 GYE.15: 13 residues within 4Å: Chain B: E.27, S.28, W.30, R.31, D.104, R.105, F.123, P.158, R.162, F.186, N.212, D.240, C.260 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:W.30, B:F.123 Hydrogen bonds: B:E.27, B:E.27, B:S.28, B:R.31, B:D.104, B:R.162, B:R.162, B:N.212, B:D.240, B:D.240 Salt bridges: B:R.31, B:R.105 GYE.24: 13 residues within 4Å: Chain C: E.27, S.28, W.30, R.31, D.104, R.105, F.123, P.158, R.162, F.186, N.212, D.240, C.260 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:F.123, C:P.158 Hydrogen bonds: C:S.28, C:S.28, C:R.31, C:D.104, C:R.105, C:R.162, C:R.162, C:N.212, C:D.240, C:D.240 Salt bridges: C:R.31, C:R.105 GYE.30: 13 residues within 4Å: Chain D: E.27, S.28, W.30, R.31, D.104, R.105, F.123, P.158, R.162, F.186, N.212, D.240, C.260 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:W.30, D:F.123 Hydrogen bonds: D:E.27, D:E.27, D:S.28, D:R.31, D:D.104, D:R.162, D:R.162, D:N.212, D:D.240, D:D.240 Salt bridges: D:R.31, D:R.105

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, M. et al., Detection and Characterization of a Mycobacterial L-Arabinofuranose ABC Transporter Identified with a Rapid Lipoproteomics Protocol. Cell Chem Biol (2019)

Release Date

2019-05-01

Peptides

Periplasmic binding protein/LacI transcriptional regulator: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Periplasmic binding protein/LacI transcriptional regulator