MolNFT v1 · #181136 · protein
Kpc-2 F72Y mutant with acylated imipenem
7LLH · Carbapenem-hydrolyzing beta-lactamase kpc: “Kpc-2 F72Y mutant with acylated imipenem”. X-ray diffraction, 1 ligand (IM2), 4 pockets (best druggability 0.39). MolNFT v1 #181136 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7LLH
- Type
- protein
- Length
- 520 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carbapenem-hydrolyzing beta-lactamase kpc
- EC
- 3.5.2.6
- UniProt
- Q9F663
- Ligands
- IM2
- Pockets
- 4 · best druggability 0.39
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Carbapenem-hydrolyzing beta-lactamase kpc (EC 3.5.2.6) | protein | 260 | 43% helix, 17% strand | Q9F663 |
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 · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 118 | 0.39 | 0.74 | 20 | empty |
| 2 | 98 | 0.38 | 0.76 | 18 | IM2 |
| 3 | 64 | 0.37 | 0.78 | 18 | empty |
| 4 | 105 | 0.37 | 0.75 | 19 | IM2 |
Interfaces
1 interface between chains.
- A–B · 394 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 disulfide (covalent ligand, disulfide).
Compared structures
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 Q9F663
- Elsewhere: RCSB PDB 7LLH · PDBe 7LLH · UniProt Q9F663
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