MolNFT v1 · #144611 · protein
Structure of goxa from pseudoalteromonas luteoviolacea
6BYW: “Structure of goxa from pseudoalteromonas luteoviolacea”. X-ray diffraction, 2 ligands (MG, SO4), 20 pockets (best druggability 0.86). MolNFT v1 #144611 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6BYW
- Type
- protein
- Length
- 3,122 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Goxa
- UniProt
- A0A161XU12
- Ligands
- MG, SO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Goxa | protein | 781 | 32% helix, 21% strand | A0A161XU12 |
| A | Goxa | protein | 787 | 33% helix, 21% strand | A0A161XU12 |
| C | Goxa | protein | 778 | 33% helix, 21% strand | A0A161XU12 |
| D | Goxa | protein | 776 | 32% helix, 21% strand | A0A161XU12 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains B, A, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains B, C
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains B, A, C, D
- EDO · 1,2-ethanediol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 548 | 0.86 | 0.92 | 58 | empty |
| 2 | 533 | 0.86 | 0.91 | 53 | empty |
| 3 | 939 | 0.80 | 0.82 | 90 | empty |
| 4 | 537 | 0.78 | 0.85 | 68 | empty |
| 5 | 144 | 0.77 | 0.94 | 25 | empty |
Interfaces
6 interfaces between chains.
- C–D · 3041 Ų buried · 55 hydrogen bonds · protein-protein
- B–A · 3031 Ų buried · 56 hydrogen bonds · protein-protein
- B–D · 2237 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 2171 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 379 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (cofactor).
Compared structures
- 6BYW · Structure of GoxA from Pseudoalteromonas luteoviolacea · the same entry in another collection · chain B against B, 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 A0A161XU12
- Elsewhere: RCSB PDB 6BYW · PDBe 6BYW · UniProt A0A161XU12
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