SMTL ID : 4pe3.1

CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM RHODOBACTER SPHAEROIDES (Rsph17029_3620, TARGET EFI-510199), APO OPEN STRUCTURE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

monomer

Ligands

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.1: 4 residues within 4Å: Chain A: N.194, L.195, P.196, E.199 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.199 IMD.2: 6 residues within 4Å: Chain A: S.218, D.222, R.281, E.284, A.285 Ligands: ZN.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.284

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

EDO.3: 10 residues within 4Å: Chain A: D.118, P.119, L.154, Y.234, P.235, G.236, L.278, H.279, D.282, L.283 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.234, A:D.282 Water bridges: A:L.154, A:H.279

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

ACT.4: 11 residues within 4Å: Chain A: P.81, H.92, T.96, F.99, R.102, F.106, M.135, I.139, Y.142, L.144, E.244 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.81, A:F.99, A:F.106, A:I.139 Salt bridges: A:H.92

10 x ZN: ZINC ION(Non-covalent)

ZN.5: 5 residues within 4Å: Chain A: E.155, D.213, Y.214, S.215, S.239 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.155, A:D.213, A:Y.214, H2O.8, H2O.9 ZN.6: 2 residues within 4Å: Chain A: H.31, L.259 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.31, H2O.14, H2O.15 ZN.7: 2 residues within 4Å: Chain A: D.222 Ligands: IMD.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.222, A:D.222 ZN.8: 1 residues within 4Å: Chain A: D.227 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.227, H2O.1 ZN.9: 3 residues within 4Å: Chain A: D.276, H.279, Q.280 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.279, H2O.2 ZN.10: 2 residues within 4Å: Chain A: D.339, K.340 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.339, A:D.339, H2O.4 ZN.11: 2 residues within 4Å: Chain A: E.284, E.287 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.287, A:E.287, H2O.2 ZN.12: 5 residues within 4Å: Chain A: T.165, S.301, E.303, E.304, K.307 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.303, A:E.303, A:E.304, H2O.5 ZN.13: 2 residues within 4Å: Chain A: T.165, D.168 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.168, H2O.1 ZN.14: 2 residues within 4Å: Chain A: P.235, D.299 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.299, A:D.299, H2O.11, H2O.16, H2O.16

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vetting, M.W. et al., Experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes. Biochemistry (2015)

Release Date

2014-05-14

Peptides

TRAP dicarboxylate transporter-DctP subunit: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

TRAP dicarboxylate transporter-DctP subunit