MolNFT v1 · #179968 · protein
Crystal structure of an essential ribosomal processing protease prp from S. aureus in complex with a covalently linked product peptide
7KLD · Phage-related ribosomal protease: “Crystal structure of an essential ribosomal processing protease prp from S. aureus in complex with a…”. X-ray diffraction, 1 ligand (CA), 1 pocket (best druggability 0.37). MolNFT v1 #179968 on…
- PDB
- 7KLD
- Type
- protein
- Length
- 332 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phage-related ribosomal protease; Lys-leu-asn-leu-gln-phe-pcs
- UniProt
- W8U5D2
- Ligands
- CA
- Pockets
- 1 · best druggability 0.37
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phage-related ribosomal protease | protein | 100 | 40% helix, 28% strand | W8U5D2 |
| B, D | Phage-related ribosomal protease | protein | 106 | 38% helix, 26% strand | W8U5D2 |
| C, Q | Lys-leu-asn-leu-gln-phe-pcs | protein | 7 | 0% helix, 0% strand | — |
| E | Lys-leu-asn-leu-gln-phe-pcs | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 8 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 94 | 0.37 | 0.76 | 22 | empty |
Interfaces
7 interfaces between chains.
- B–D · 896 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 596 Ų buried · 12 hydrogen bonds · protein-protein
- A–Q · 530 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 528 Ų buried · 5 hydrogen bonds · protein-protein
- D–E · 515 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (nonstandard).
Compared structures
- 7KLD · Crystal Structure of an Essential Ribosomal Processing Protease Prp from S. aureus in… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt W8U5D2
- Elsewhere: RCSB PDB 7KLD · PDBe 7KLD · UniProt W8U5D2
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