Research workbench
Xray structure of GAG133-278
Analyse Xray structure of GAG133-278 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GON
- Type
- protein
- Length
- 531 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein P24 (ca)
- UniProt
- P12497
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 63% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein P24 (ca) | protein | 127 | 65% helix, 0% strand | P12497 |
| B | Capsid protein P24 (ca) | protein | 137 | 61% helix, 0% strand | P12497 |
| C | Capsid protein P24 (ca) | protein | 138 | 61% helix, 4% strand | P12497 |
| D | Capsid protein P24 (ca) | protein | 129 | 64% helix, 0% strand | P12497 |
Ligands and binding sites
- FLC · Citrate anion · additive · 2 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 629 | 0.69 | 0.77 | 60 | FLC |
| 2 | 346 | 0.61 | 0.78 | 37 | empty |
| 3 | 115 | 0.44 | 0.78 | 29 | empty |
| 4 | 65 | 0.33 | 0.76 | 14 | empty |
| 5 | 58 | 0.30 | 0.75 | 18 | empty |
Interfaces
3 interfaces between chains.
- C–D · 506 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 291 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 260 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 modified (engineered).
Compared structures
- 2GON · Xray Structure of Gag133-278 · 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 P12497
- Elsewhere: RCSB PDB 2GON · PDBe 2GON · UniProt P12497
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