SMTL ID : 7kld.1

Crystal Structure of an Essential Ribosomal Processing Protease Prp from S. aureus in complex with a covalently linked product Peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-hexamer

Ligands

6 x LYS- LEU- ASN- LEU- GLN- PHE- PCS: LYS-LEU-ASN-LEU-GLN-PHE-PCS(Non-covalent)

LYS-LEU-ASN-LEU-GLN-PHE-PCS.1: 24 residues within 4Å: Chain B: I.2, M.19, D.20, G.21, H.22, A.23, Y.28, G.29, H.30, D.31, C.34, A.35, A.37, S.38, A.39, L.41, F.42, Y.60, D.61, D.62, G.64, G.65, H.66, F.67 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:I.2, B:M.19, B:A.35, B:A.39, B:F.42, B:F.42, B:F.67 Hydrogen bonds: B:A.23, B:G.29, B:H.30, B:D.31, B:D.31, B:A.35, B:S.38, B:S.38, B:G.65 pi-Stacking: B:F.42 LYS-LEU-ASN-LEU-GLN-PHE-PCS.2: 23 residues within 4Å: Chain A: I.2, M.19, D.20, G.21, H.22, A.23, H.30, D.31, I.32, C.34, A.35, A.37, S.38, A.39, L.41, F.42, N.46, Y.60, D.61, G.64, G.65, H.66, F.67 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:I.2, A:M.19, A:A.35, A:A.39, A:F.42, A:F.67 Hydrogen bonds: A:A.23, A:H.30, A:D.31, A:D.31, A:A.35, A:S.38, A:S.38, A:G.65 pi-Stacking: A:F.42 LYS-LEU-ASN-LEU-GLN-PHE-PCS.9: 24 residues within 4Å: Chain D: I.2, M.19, D.20, G.21, H.22, A.23, Y.28, G.29, H.30, D.31, C.34, A.35, A.37, S.38, A.39, L.41, F.42, Y.60, D.61, D.62, G.64, G.65, H.66, F.67 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:I.2, D:M.19, D:A.35, D:A.39, D:F.42, D:F.42, D:F.67 Hydrogen bonds: D:A.23, D:G.29, D:H.30, D:D.31, D:D.31, D:A.35, D:S.38, D:S.38, D:G.65 pi-Stacking: D:F.42 LYS-LEU-ASN-LEU-GLN-PHE-PCS.10: 23 residues within 4Å: Chain C: I.2, M.19, D.20, G.21, H.22, A.23, H.30, D.31, I.32, C.34, A.35, A.37, S.38, A.39, L.41, F.42, N.46, Y.60, D.61, G.64, G.65, H.66, F.67 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:I.2, C:M.19, C:A.35, C:A.39, C:F.42, C:F.67 Hydrogen bonds: C:A.23, C:D.31, C:D.31, C:A.35, C:S.38, C:S.38, C:G.65 Water bridges: C:H.30 pi-Stacking: C:F.42 LYS-LEU-ASN-LEU-GLN-PHE-PCS.17: 24 residues within 4Å: Chain E: I.2, M.19, G.21, H.22, A.23, Y.28, G.29, H.30, D.31, C.34, A.35, A.37, S.38, A.39, L.41, F.42, Y.60, D.61, D.62, N.63, G.64, G.65, H.66, F.67 15 PLIP interactions: 15 interactions with chain E Hydrophobic interactions: E:I.2, E:M.19, E:A.35, E:A.39, E:F.42, E:F.42, E:F.67 Hydrogen bonds: E:A.23, E:G.29, E:D.31, E:D.31, E:S.38, E:S.38, E:G.65 Water bridges: E:D.24 LYS-LEU-ASN-LEU-GLN-PHE-PCS.20: 24 residues within 4Å: Chain F: I.2, M.19, G.21, H.22, A.23, Y.28, G.29, H.30, D.31, C.34, A.35, A.37, S.38, A.39, L.41, F.42, Y.60, D.61, D.62, N.63, G.64, G.65, H.66, F.67 15 PLIP interactions: 15 interactions with chain F Hydrophobic interactions: F:I.2, F:M.19, F:A.35, F:A.39, F:F.42, F:F.42, F:F.67 Hydrogen bonds: F:A.23, F:G.29, F:D.31, F:D.31, F:S.38, F:S.38, F:G.65 Water bridges: F:D.24

16 x CA: CALCIUM ION(Non-covalent)

CA.3: 3 residues within 4Å: Chain A: N.104, Y.105 Chain D: D.10 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Metal complexes: A:Y.105, D:D.10 CA.4: 2 residues within 4Å: Chain A: L.51, E.78 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:L.51, H2O.1 CA.5: 4 residues within 4Å: Chain A: D.57, N.59, H.68 Chain B: D.20 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Metal complexes: B:D.20, B:D.20, A:D.57, A:D.57 CA.6: 6 residues within 4Å: Chain A: M.1, E.94, N.98, I.101, R.102 Chain D: E.11 5 PLIP interactions: 1 interactions with chain D, 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: D:E.11, A:E.94, A:N.98, A:I.101, H2O.4 CA.7: 2 residues within 4Å: Chain B: L.51, E.78 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:L.51, B:E.78, H2O.2, H2O.3 CA.8: 3 residues within 4Å: Chain A: D.20 Chain B: D.57, N.59 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:D.57, B:D.57, A:D.20, H2O.1 CA.11: 3 residues within 4Å: Chain B: D.10 Chain C: N.104, Y.105 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Metal complexes: C:Y.105, B:D.10 CA.12: 2 residues within 4Å: Chain C: L.51, E.78 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:L.51, H2O.4 CA.13: 4 residues within 4Å: Chain C: D.57, N.59, H.68 Chain D: D.20 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Metal complexes: C:D.57, C:D.57, D:D.20, D:D.20 CA.14: 6 residues within 4Å: Chain B: E.11 Chain C: M.1, E.94, N.98, I.101, R.102 5 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: C:E.94, C:N.98, C:I.101, B:E.11, H2O.2 CA.15: 2 residues within 4Å: Chain D: L.51, E.78 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:L.51, D:E.78, H2O.4, H2O.5 CA.16: 3 residues within 4Å: Chain C: D.20 Chain D: D.57, N.59 4 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: D:D.57, D:D.57, C:D.20, H2O.3 CA.18: 5 residues within 4Å: Chain E: D.57, N.59, H.68 Chain F: D.20, H.66 5 PLIP interactions: 2 interactions with chain E, 2 interactions with chain F, 1 Ligand-Water interactions Metal complexes: E:D.57, E:D.57, F:D.20, F:D.20, H2O.5 CA.19: 4 residues within 4Å: Chain C: V.8, N.9, K.106 Chain E: D.10 5 PLIP interactions: 1 interactions with chain E, 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: E:D.10, C:V.8, H2O.3, H2O.3, H2O.3 CA.21: 5 residues within 4Å: Chain E: D.20, H.66 Chain F: D.57, N.59, H.68 5 PLIP interactions: 2 interactions with chain E, 2 interactions with chain F, 1 Ligand-Water interactions Metal complexes: E:D.20, E:D.20, F:D.57, F:D.57, H2O.6 CA.22: 4 residues within 4Å: Chain A: V.8, N.9, K.106 Chain F: D.10 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: A:V.8, F:D.10, H2O.1, H2O.1, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hotinger, J.A. et al., Phage-Related Ribosomal Protease (Prp) of Staphylococcus aureus : In Vitro Michaelis-Menten Kinetics, Screening for Inhibitors, and Crystal Structure of a Covalent Inhibition Product Complex. Biochemistry (2022)

Release Date

2021-09-01

Peptides

Phage-related ribosomal protease: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
D

F
D

Phage-related ribosomal protease

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