SMTL ID : 8ono.1

Modified oligopeptidase B from S. proteamaculans in intermediate conformation with 5 spermine molecule at 1.65 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

5 x SPM: SPERMINE(Non-covalent)

SPM.1: 4 residues within 4Å: Chain A: Y.80, Y.100, L.132, Y.366 1 PLIP interactions: 1 interactions with chain A Water bridges: A:L.132 SPM.2: 6 residues within 4Å: Chain A: Y.80, V.81, Q.105, Y.366, P.368, R.376 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.81, A:V.81, A:Y.366 Hydrogen bonds: A:R.376 Water bridges: A:V.78, A:Q.105, A:Q.105, A:N.367, A:E.369, A:E.369 SPM.3: 5 residues within 4Å: Chain A: F.440, R.442, A.517, Q.518, Y.520 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.442, A:R.442, A:A.517 Water bridges: A:Y.435, A:Q.518 SPM.4: 7 residues within 4Å: Chain A: Y.450, Y.452, S.457, S.458, M.459, G.531, S.532 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.452 Hydrogen bonds: A:Y.450, A:S.458, A:S.458, A:G.531 Water bridges: A:R.333 SPM.5: 3 residues within 4Å: Chain A: M.459, D.460, Y.669 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.669 Water bridges: A:S.464, A:S.464, A:S.466, A:R.467, A:R.467, A:R.467

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Petrenko, D.E. et al., Modified oligopeptidase B from S. proteomaculans in intermediate conformation with 5 spermine molecule at 1.65 A resolution. To Be Published

Release Date

2023-05-31

Peptides

Oligopeptidase B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Oligopeptidase B

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