SMTL ID : 5t88.2 (1 other biounit)

Prolyl oligopeptidase from Pyrococcus furiosus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

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

CL.1: 6 residues within 4Å: Chain A: W.474, R.476, Y.555, R.600, L.604, L.607 Ligand excluded by PLIP CL.2: 5 residues within 4Å: Chain A: R.476, Y.501, M.593, R.600, E.603 Ligand excluded by PLIP

6 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.3: 2 residues within 4Å: Chain A: K.529, E.532 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.529 TRS.4: 8 residues within 4Å: Chain A: M.1, L.507, R.508, H.510, K.511, P.525, E.526, R.531 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:M.1, A:R.508, A:H.510, A:K.511 Water bridges: A:E.526, A:E.526 TRS.5: 13 residues within 4Å: Chain A: M.53, G.99, F.100, T.101, A.110, Y.111, S.112, T.123, S.140, I.141, W.142, N.143, I.144 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.110, A:S.112, A:T.123, A:N.143, A:I.144 Water bridges: A:F.100 TRS.6: 4 residues within 4Å: Chain A: K.394, K.466, E.467, G.468 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.394 TRS.7: 2 residues within 4Å: Chain A: E.312, K.313 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.312, A:E.312 TRS.8: 6 residues within 4Å: Chain A: A.374, T.375, A.459, E.462, K.463, K.466 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.375, A:T.375, A:A.459, A:K.466

2 x PRO: PROLINE(Non-covalent)

PRO.9: 6 residues within 4Å: Chain A: Y.401, F.404, I.406, W.518, R.562 Ligands: PRO.10 3 PLIP interactions: 3 interactions with chain A, Hydrogen bonds: A:Y.401, A:W.518, A:R.562 PRO.10: 10 residues within 4Å: Chain A: Y.401, F.404, S.477, N.478, V.503, W.518, Y.522, R.562, V.563 Ligands: PRO.9 7 PLIP interactions: 7 interactions with chain A, Hydrophobic interactions: A:F.404, A:N.478 Hydrogen bonds: A:S.477, A:W.518, A:R.562, A:R.562 Salt bridges: A:R.562

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ellis-Guardiola, K. et al., Crystal Structure and Conformational Dynamics of Pyrococcus furiosus Prolyl Oligopeptidase. Biochemistry (2019)

Release Date

2017-09-06

Peptides

Prolyl endopeptidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Prolyl endopeptidase

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