MolNFT v1 · #143514 · protein
Crystal structure kpc-2 beta-lactamase complexed with wck 5153 by soaking
6B1X · Carbapenem-hydrolyzing beta-lactamase kpc: “Crystal structure kpc-2 beta-lactamase complexed with wck 5153 by soaking”. X-ray diffraction, 1 ligand (C9D), 4 pockets (best druggability 0.49). MolNFT v1 #143514 on GenesisL1: 3D…
- PDB
- 6B1X
- Type
- protein
- Length
- 533 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
- C9D
- Pockets
- 4 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carbapenem-hydrolyzing beta-lactamase kpc (EC 3.5.2.6) | protein | 268 | 44% helix, 17% strand | Q9F663 |
| B | Carbapenem-hydrolyzing beta-lactamase kpc (EC 3.5.2.6) | protein | 265 | 43% helix, 17% strand | Q9F663 |
Ligands and binding sites
- C9D · (2S,5R)-1-formyl-N'-[(3R)-pyrrolidine-3-carbonyl]-5-[(sulfooxy)amino]piperidine-2-carbohydrazide · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B
- CIT · Citric acid · additive · 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 | 171 | 0.49 | 0.77 | 28 | CIT |
| 2 | 103 | 0.40 | 0.76 | 21 | CIT, EDO |
| 3 | 99 | 0.36 | 0.75 | 17 | C9D |
| 4 | 93 | 0.35 | 0.75 | 18 | C9D |
Interfaces
1 interface between chains.
- A–B · 473 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 disulfide (covalent ligand, disulfide).
Compared structures
- 6B1X · Crystal structure KPC-2 beta-lactamase complexed with WCK 5153 by soaking · 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 B 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 6B1X · PDBe 6B1X · UniProt Q9F663
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