MolNFT v1 · #181319 · protein
Crystal structure of kpc-2 S70G/T215P mutant with hydrolyzed imipenem
7LR9 · Carbapenem-hydrolyzing beta-lactamase kpc: “Crystal structure of kpc-2 S70G/T215P mutant with hydrolyzed imipenem”. X-ray diffraction, 1 ligand (8YF), 4 pockets (best druggability 0.48). MolNFT v1 #181319 on GenesisL1: 3D structure…
- PDB
- 7LR9
- Type
- protein
- Length
- 528 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
- 8YF
- Pockets
- 4 · best druggability 0.48
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Carbapenem-hydrolyzing beta-lactamase kpc (EC 3.5.2.6) | protein | 264 | 44% helix, 17% strand | Q9F663 |
Ligands and binding sites
- 8YF · (2R)-2-[(2S,3R)-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-4-(2-methanimidamidoethylsulfanyl)-2,3-dihydro-1H-pyrrole-5-carboxylic 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 | 164 | 0.48 | 0.77 | 31 | 8YF |
| 2 | 90 | 0.34 | 0.74 | 20 | 8YF |
| 3 | 55 | 0.31 | 0.75 | 15 | empty |
| 4 | 72 | 0.31 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 19 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7LR9 · Crystal structure of KPC-2 S70G/T215P mutant with hydrolyzed imipenem · the same entry in another collection · chain A against A, TM-score 1.00
- Q9F663 · AlphaFold monomer V2.0 prediction for carbapenem-hydrolyzing beta- lactamase kpc (Q9F663) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 7LR9 · PDBe 7LR9 · UniProt Q9F663
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