MolNFT v1 · #171058 · protein
Structure of a new variant of gnca ancestral beta-lactamase
6YRS: “Structure of a new variant of gnca ancestral beta-lactamase”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.60). MolNFT v1 #171058 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6YRS
- Type
- protein
- Length
- 504 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ancestral beta-lactamase
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ancestral beta-lactamase | protein | 264 | 44% helix, 17% strand | — |
| B | Ancestral beta-lactamase | protein | 240 | 48% helix, 16% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B
- PGE · Triethylene glycol · additive · 5 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 352 | 0.60 | 0.77 | 43 | PGE, EDO |
| 2 | 92 | 0.37 | 0.76 | 18 | ACT, PGE, SO4 |
| 3 | 52 | 0.31 | 0.76 | 11 | PGE |
| 4 | 69 | 0.30 | 0.74 | 15 | empty |
| 5 | 59 | 0.28 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 298 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6YRS · Structure of a new variant of GNCA ancestral beta-lactamase · 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 6YRS · PDBe 6YRS
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