SMTL ID : 5jd8.1

Crystal structure of the serine endoprotease from Yersinia pestis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-trimer

Ligands

3 x CXS: 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID(Non-covalent)

CXS.1: 5 residues within 4Å: Chain A: A.73, E.74, I.76, E.87, A.88 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.76 CXS.4: 5 residues within 4Å: Chain B: A.73, E.74, I.76, E.87, A.88 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.76 CXS.7: 5 residues within 4Å: Chain C: A.73, E.74, I.76, E.87, A.88 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.76

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 5 residues within 4Å: Chain A: V.16, P.17, T.18, S.19, Y.20 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:T.18, C:T.18, A:S.19 PEG.5: 5 residues within 4Å: Chain B: V.16, P.17, T.18, S.19, Y.20 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.19, A:T.18, A:T.18 PEG.8: 5 residues within 4Å: Chain C: V.16, P.17, T.18, S.19, Y.20 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:S.19, B:T.18, B:T.18

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 11 residues within 4Å: Chain A: Y.20, V.125, Q.141 Chain B: Y.20, V.125, Q.141 Chain C: Y.20, V.125, Q.141 Ligands: SO4.6, SO4.9 6 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C, 2 interactions with chain A Hydrogen bonds: B:Y.20, B:Q.141, C:Y.20, C:Q.141, A:Y.20, A:Q.141 SO4.6: 11 residues within 4Å: Chain A: Y.20, V.125, Q.141 Chain B: Y.20, V.125, Q.141 Chain C: Y.20, V.125, Q.141 Ligands: SO4.3, SO4.9 6 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C, 2 interactions with chain A Hydrogen bonds: B:Y.20, B:Q.141, C:Y.20, C:Q.141, A:Y.20, A:Q.141 SO4.9: 11 residues within 4Å: Chain A: Y.20, V.125, Q.141 Chain B: Y.20, V.125, Q.141 Chain C: Y.20, V.125, Q.141 Ligands: SO4.3, SO4.6 6 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C, 2 interactions with chain A Hydrogen bonds: B:Y.20, B:Q.141, C:Y.20, C:Q.141, A:Y.20, A:Q.141

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Filippova, E.V. et al., Crystal structure of the serine endoprotease from Yersinia pestis. To Be Published

Release Date

2016-05-04

Peptides

Periplasmic serine peptidase DegS: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Periplasmic serine peptidase DegS