Research workbench
Serine beta-lactamase kpc-2 in complex with dual MBL/SBL inhibitor MS05
Analyse Serine beta-lactamase kpc-2 in complex with dual MBL/SBL inhibitor MS05 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JN3
- Type
- protein
- Length
- 1,050 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
- BX6
- Pockets
- 10 · best druggability 0.73
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 | 264 | 42% helix, 17% strand | Q93LQ9 |
| B | Serine beta-lactamase kpc-2 (EC 3.5.2.6) | protein | 263 | 42% 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
- BX6 · [(1R)-1-[[(2S)-2-methyl-3-sulfanyl-propanoyl]amino]-2-phenyl-ethyl]boronic acid · ligand · 4 copies · chains A, B, C, D
- ACY · Acetic acid · additive · 7 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 618 | 0.73 | 0.80 | 72 | BX6, ACY |
| 2 | 696 | 0.68 | 0.76 | 72 | empty |
| 3 | 279 | 0.61 | 0.80 | 48 | empty |
| 4 | 255 | 0.60 | 0.80 | 42 | empty |
| 5 | 103 | 0.36 | 0.75 | 18 | BX6, ACY |
Interfaces
5 interfaces between chains.
- A–B · 835 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 785 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 434 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 338 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 166 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 6JN3 · Serine Beta-Lactamase KPC-2 in Complex with Dual MBL/SBL Inhibitor MS05 · 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 6JN3 · PDBe 6JN3 · UniProt Q93LQ9
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