MolNFT v1 · #153715 · protein
Serine beta-lactamase kpc-2 in complex with dual MBL/SBL inhibitor MS23
6JN5: “Serine beta-lactamase kpc-2 in complex with dual MBL/SBL inhibitor MS23”. X-ray diffraction, 1 ligand (BXU), 11 pockets (best druggability 0.78). MolNFT v1 #153715 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6JN5
- Type
- protein
- Length
- 1,045 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
- BXU
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Serine beta-lactamase kpc-2 (EC 3.5.2.6) | protein | 263 | 43% helix, 17% strand | Q93LQ9 |
| B | Serine beta-lactamase kpc-2 (EC 3.5.2.6) | protein | 260 | 43% helix, 17% strand | Q93LQ9 |
| D | Serine beta-lactamase kpc-2 (EC 3.5.2.6) | protein | 259 | 44% helix, 17% strand | Q93LQ9 |
Ligands and binding sites
- BXU · [(S)-(4-fluorophenyl)-[[(2S)-2-methyl-3-sulfanyl-propanoyl]amino]methyl]boronic acid · ligand · 4 copies · chains A, B, C, 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 | 627 | 0.78 | 0.83 | 62 | empty |
| 2 | 242 | 0.61 | 0.81 | 35 | empty |
| 3 | 225 | 0.60 | 0.81 | 41 | empty |
| 4 | 109 | 0.54 | 0.83 | 24 | empty |
| 5 | 51 | 0.42 | 0.83 | 14 | empty |
Interfaces
5 interfaces between chains.
- C–D · 810 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 779 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 338 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 229 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 160 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 6JN5 · Serine Beta-Lactamase KPC-2 in Complex with Dual MBL/SBL Inhibitor MS23 · 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 6JN5 · PDBe 6JN5 · UniProt Q93LQ9
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