SMTL ID : 5f1q.2 (1 other biounit)

Crystal Structure of Periplasmic Dipeptide Transport Protein from Yersinia pestis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

monomer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: P.380, T.411, Y.412, E.413 No protein-ligand interaction detected (PLIP) EDO.2: 2 residues within 4Å: Chain A: D.320, A.333 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.320 EDO.4: 4 residues within 4Å: Chain A: K.350, D.351, Y.352, N.495 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.350, A:N.495 Water bridges: A:A.353 EDO.5: 5 residues within 4Å: Chain A: M.285, E.286, Q.287, V.520, V.521 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.286, A:V.521 EDO.8: 5 residues within 4Å: Chain A: G.37, S.38, I.246, P.248, V.381 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.38, A:S.38 Water bridges: A:S.38, A:S.38, A:W.414 EDO.9: 3 residues within 4Å: Chain A: P.340, T.341, M.342 No protein-ligand interaction detected (PLIP) EDO.10: 2 residues within 4Å: Chain A: Q.287, P.288 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.288 EDO.11: 4 residues within 4Å: Chain A: E.286, Q.287, P.288, T.507 No protein-ligand interaction detected (PLIP)

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

CL.3: 5 residues within 4Å: Chain A: A.334, K.335, N.336, Y.345, H.505 Ligand excluded by PLIP

2 x GLN: GLUTAMINE(Non-covalent)

GLN.6: 10 residues within 4Å: Chain A: T.48, G.50, Y.142, W.433, T.434, D.436, L.524, G.525, K.526 Ligands: GLN.7 7 PLIP interactions: 5 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:G.50, A:Y.142, A:T.434, A:D.436, Q.6, Q.6 Water bridges: A:D.436 GLN.7: 13 residues within 4Å: Chain A: T.48, S.49, G.50, R.383, Y.385, W.414, L.418, M.431, G.432, W.433, S.457, Y.459 Ligands: GLN.6 12 PLIP interactions: 11 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:W.433 Hydrogen bonds: A:T.48, A:T.48, A:G.50, A:Y.385, A:Y.385, A:S.457, A:Y.459, Q.6 Water bridges: A:T.434, A:T.434 Salt bridges: A:R.383

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y. et al., Crystal Structure of Periplasmic Dipeptide Transport Protein from Yersinia pestis. To Be Published

Release Date

2015-12-23

Peptides

Periplasmic dipeptide transport protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Periplasmic dipeptide transport protein

Related Entries With Identical Sequence