MolNFT v1 · #168110 · protein
Class D beta-lactamase bat-2 delta mutant
6W5O · Bat-2 beta-lactamase delta mutant: “Class D beta-lactamase bat-2 delta mutant”. X-ray diffraction, 20 pockets (best druggability 0.71). MolNFT v1 #168110 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6W5O
- Type
- protein
- Length
- 1,872 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bat-2 beta-lactamase delta mutant
- EC
- 3.5.2.6
- UniProt
- A0A0H3EA14
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Bat-2 beta-lactamase delta mutant (EC 3.5.2.6) | protein | 234 | 38% helix, 20% strand | A0A0H3EA14 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 700 | 0.71 | 0.78 | 43 | empty |
| 2 | 651 | 0.69 | 0.77 | 42 | empty |
| 3 | 706 | 0.69 | 0.77 | 44 | empty |
| 4 | 680 | 0.69 | 0.77 | 37 | empty |
| 5 | 584 | 0.67 | 0.77 | 84 | FLC |
Interfaces
8 interfaces between chains.
- F–H · 1134 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1123 Ų buried · 18 hydrogen bonds · protein-protein
- E–G · 1103 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 1091 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 564 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (carboxylation).
Compared structures
- 6W5O · Class D beta-lactamase BAT-2 delta mutant · 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 A0A0H3EA14
- Elsewhere: RCSB PDB 6W5O · PDBe 6W5O · UniProt A0A0H3EA14
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