MolNFT v1 · #165496 · protein
Variant W229D/F290W-12 of the last common ancestor of gram-negative bacteria beta-lactamase class a (GNCA4)
6TXD · Beta lactamase (GNCA4-12): “Variant W229D/F290W-12 of the last common ancestor of gram-negative bacteria beta-lactamase class a (GNCA4)”. X-ray diffraction, 1 ligand (NA), 10 pockets (best druggability 0.71). MolNFT v1 #165496 on…
- PDB
- 6TXD
- Type
- protein
- Length
- 797 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta lactamase (GNCA4-12)
- Ligands
- NA
- Pockets
- 10 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta lactamase (GNCA4-12) | protein | 266 | 45% helix, 17% strand | — |
| C | Beta lactamase (GNCA4-12) | protein | 265 | 46% helix, 18% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · chains A
- FMT · Formic acid · additive · 8 copies · chains A, B, C
- ACT · Acetate ion · additive · 4 copies · chains A, C, B
- GOL · Glycerol · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 927 | 0.71 | 0.76 | 70 | FMT |
| 2 | 426 | 0.65 | 0.78 | 57 | FMT, GOL |
| 3 | 401 | 0.65 | 0.79 | 48 | ACT |
| 4 | 410 | 0.64 | 0.78 | 56 | ACT, GOL, FMT |
| 5 | 87 | 0.52 | 0.83 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 487 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 476 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 460 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6TXD · Variant W229D/F290W-12 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 6TXD · PDBe 6TXD
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