MolNFT v1 · #156968 · protein
Crystal structure of pencillin binding protein 4 (PBP4) from enterococcus faecalis in the imipenem-bound form
6MKH: “Crystal structure of pencillin binding protein 4 (PBP4) from enterococcus faecalis in the imipenem-bound form”. X-ray diffraction, 2 ligands (IM2, PO4), 3 pockets (best druggability 0.44). MolNFT v1 #156968 on GenesisL1: 3D…
- PDB
- 6MKH
- Type
- protein
- Length
- 445 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pencillin binding protein 4 (PBP4)
- UniProt
- Q9K3C9
- Ligands
- IM2, PO4
- Pockets
- 3 · best druggability 0.44
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pencillin binding protein 4 (PBP4) | protein | 445 | 34% helix, 20% strand | Q9K3C9 |
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
- PO4 · Phosphate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 164 | 0.44 | 0.75 | 31 | empty |
| 2 | 148 | 0.43 | 0.75 | 25 | IM2 |
| 3 | 58 | 0.30 | 0.75 | 16 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6MKH · Crystal structure of pencillin binding protein 4 (PBP4) from Enterococcus faecalis 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 Q9K3C9
- Elsewhere: RCSB PDB 6MKH · PDBe 6MKH · UniProt Q9K3C9
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