MolNFT v1 · #156967 · protein
Crystal structure of penicillin binding protein 5 (PBP5) from enterococcus faecium in the benzylpenicilin-bound form
6MKG: “Crystal structure of penicillin binding protein 5 (PBP5) from enterococcus faecium in the…”. X-ray diffraction, 2 ligands (PNM, SO4), 7 pockets (best druggability 0.49). MolNFT v1 #156967 on GenesisL1: 3D structure, binding sites…
- PDB
- 6MKG
- Type
- protein
- Length
- 640 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin binding protein 5 (PBP5)
- UniProt
- A0A075Q0W3
- Ligands
- PNM, SO4
- Pockets
- 7 · best druggability 0.49
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin binding protein 5 (PBP5) | protein | 640 | 33% helix, 26% strand | A0A075Q0W3 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 84 | 0.49 | 0.82 | 21 | empty |
| 2 | 162 | 0.43 | 0.74 | 25 | empty |
| 3 | 64 | 0.42 | 0.81 | 16 | empty |
| 4 | 156 | 0.42 | 0.75 | 26 | PNM |
| 5 | 67 | 0.38 | 0.78 | 18 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6MKG · Crystal structure of penicillin binding protein 5 (PBP5) from Enterococcus faecium in the… · 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 A0A075Q0W3
- Elsewhere: RCSB PDB 6MKG · PDBe 6MKG · UniProt A0A075Q0W3
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