Research workbench
Variant W229D/F290W-2 of the last common ancestor of gram-negative bacteria beta-lactamase class a (GNCA4) bound to 5(6)- nitrobenzotriazole (ts-analog)
Analyse Variant W229D/F290W-2 of the last common ancestor of gram-negative bacteria… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TY6
- Type
- protein
- Length
- 796 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta lactamase (GNCA4-2)
- Ligands
- 6NT, NA
- Pockets
- 11 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Beta lactamase (GNCA4-2) | protein | 265 | 45% helix, 17% strand | — |
| B | Beta lactamase (GNCA4-2) | protein | 266 | 46% helix, 17% strand | — |
Ligands and binding sites
- 6NT · 6-nitrobenzotriazole · ligand · 3 copies · chains A, B, C
- NA · Sodium ion · metal · chains A
- FMT · Formic acid · additive · 17 copies · chains A, C, B
- GOL · Glycerol · additive · 5 copies · chains A, B, C
- ACT · Acetate ion · additive · 5 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 943 | 0.71 | 0.76 | 68 | FMT |
| 2 | 387 | 0.65 | 0.79 | 46 | ACT, GOL |
| 3 | 362 | 0.63 | 0.79 | 50 | ACT, FMT |
| 4 | 124 | 0.60 | 0.85 | 24 | 6NT |
| 5 | 127 | 0.58 | 0.84 | 22 | 6NT |
Interfaces
3 interfaces between chains.
- B–C · 490 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 473 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 466 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6TY6 · Variant W229D/F290W-2 of the last common ancestor of Gram-negative bacteria… · 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
- Elsewhere: RCSB PDB 6TY6 · PDBe 6TY6
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