MolNFT v1 · #168498 · protein
Class C beta-lactamase from acinetobacter baumannii in complex with 4- (ETHYL(METHYL)CARBAMOYL)PHENYL boronic acid
6WIF: “Class C beta-lactamase from acinetobacter baumannii in complex with 4- (ETHYL(METHYL)CARBAMOYL)PHENYL boronic…”. X-ray diffraction, 2 ligands (U2Y, CL), 11 pockets (best druggability 0.76). MolNFT v1 #168498 on GenesisL1: 3D…
- PDB
- 6WIF
- Type
- protein
- Length
- 1,428 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- D6NSN2
- Ligands
- U2Y, CL
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 355 | 40% helix, 20% strand | D6NSN2 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 359 | 41% helix, 19% strand | D6NSN2 |
| C, D | Beta-lactamase (EC 3.5.2.6) | protein | 357 | 40% helix, 20% strand | D6NSN2 |
Ligands and binding sites
- U2Y · {4-[ethyl(methyl)carbamoyl]phenyl}boronic acid · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 3 copies · chains A, C
- EDO · 1,2-ethanediol · additive · 11 copies · chains B, C, D
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 4 copies · chains 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 674 | 0.76 | 0.81 | 66 | EDO |
| 2 | 225 | 0.62 | 0.82 | 40 | U2Y, EPE, EDO |
| 3 | 293 | 0.59 | 0.78 | 45 | U2Y, EPE |
| 4 | 304 | 0.58 | 0.77 | 42 | U2Y, EPE, CL |
| 5 | 288 | 0.57 | 0.77 | 43 | U2Y |
Interfaces
5 interfaces between chains.
- B–C · 455 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 129 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 67 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 35 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 27 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand, additive adduct).
Compared structures
- 6WIF · Class C beta-lactamase from Acinetobacter baumannii in complex with… · 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 D6NSN2
- Elsewhere: RCSB PDB 6WIF · PDBe 6WIF · UniProt D6NSN2
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