Research workbench
Crystal structure of penicillin binding protein 5 (PBP5) from enterococcus faecium in the imipenem-bound form
Analyse Crystal structure of penicillin binding protein 5 (PBP5) from enterococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MKF
- 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
- IM2, SO4
- Pockets
- 7 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin binding protein 5 (PBP5) | protein | 640 | 34% helix, 25% strand | A0A075Q0W3 |
Ligands and binding sites
- IM2 · (5R)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-[(2-{[(E)-iminomethyl]amino}ethyl)sulfanyl]-4,5-dihydro-1H-pyrrole-2-carbox ylic acid · ligand · chains A
- SO4 · Sulfate ion · ion · 15 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 113 | 0.52 | 0.82 | 24 | empty |
| 2 | 241 | 0.49 | 0.74 | 30 | empty |
| 3 | 175 | 0.43 | 0.74 | 29 | IM2 |
| 4 | 57 | 0.40 | 0.81 | 15 | empty |
| 5 | 88 | 0.34 | 0.74 | 25 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6MKF · 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 6MKF · PDBe 6MKF · UniProt A0A075Q0W3
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