MolNFT v1 · #153714 · protein
Serine beta-lactamase kpc-2 in complex with dual MBL/SBL inhibitor wl- 001
6JN4: “Serine beta-lactamase kpc-2 in complex with dual MBL/SBL inhibitor wl- 001”. X-ray diffraction, 1 ligand (BX9), 11 pockets (best druggability 0.75). MolNFT v1 #153714 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6JN4
- Type
- protein
- Length
- 1,047 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine beta-lactamase kpc-2
- EC
- 3.5.2.6
- UniProt
- Q93LQ9
- Ligands
- BX9
- Pockets
- 11 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Serine beta-lactamase kpc-2 (EC 3.5.2.6) | protein | 264 | 42% helix, 17% strand | Q93LQ9 |
| B | Serine beta-lactamase kpc-2 (EC 3.5.2.6) | protein | 262 | 44% helix, 17% strand | Q93LQ9 |
| C | Serine beta-lactamase kpc-2 (EC 3.5.2.6) | protein | 257 | 44% helix, 18% strand | Q93LQ9 |
Ligands and binding sites
- BX9 · [(R)-(4-fluorophenyl)-[[(2S)-2-methyl-3-sulfanyl-propanoyl]amino]methyl]boronic acid · ligand · 4 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 8 copies · chains A, B, C
- ACY · Acetic acid · additive · 5 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 528 | 0.75 | 0.83 | 57 | ACT |
| 2 | 202 | 0.63 | 0.83 | 36 | empty |
| 3 | 260 | 0.63 | 0.81 | 30 | empty |
| 4 | 250 | 0.62 | 0.81 | 39 | empty |
| 5 | 128 | 0.48 | 0.79 | 25 | empty |
Interfaces
5 interfaces between chains.
- A–B · 861 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 704 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 424 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 322 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 259 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 4 disulfide (covalent ligand, disulfide).
Compared structures
- 6JN4 · Serine Beta-Lactamase KPC-2 in Complex with Dual MBL/SBL Inhibitor WL-001 · 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 Q93LQ9
- Elsewhere: RCSB PDB 6JN4 · PDBe 6JN4 · UniProt Q93LQ9
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