MolNFT v1 · #176911 · protein
Crystal structure of PR55GAG-matrix domain in complex with IP6 in space group C121
7E1J · Capsid protein P24: “Crystal structure of PR55GAG-matrix domain in complex with IP6 in space group C121”. X-ray diffraction, 1 ligand (IHP), 4 pockets (best druggability 0.72). MolNFT v1 #176911 on GenesisL1: 3D structure, binding…
- PDB
- 7E1J
- Type
- protein
- Length
- 665 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein P24
- UniProt
- T2CJ20
- Ligands
- IHP
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 6 distinct chains · 65% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein P24 | protein | 116 | 68% helix, 4% strand | T2CJ20 |
| B | Capsid protein P24 | protein | 109 | 62% helix, 5% strand | T2CJ20 |
| C | Capsid protein P24 | protein | 111 | 66% helix, 5% strand | T2CJ20 |
| D | Capsid protein P24 | protein | 110 | 65% helix, 5% strand | T2CJ20 |
| E | Capsid protein P24 | protein | 108 | 64% helix, 5% strand | T2CJ20 |
| F | Capsid protein P24 | protein | 111 | 63% helix, 5% strand | T2CJ20 |
Ligands and binding sites
- IHP · Inositol hexakisphosphate · ligand · 6 copies · chains A, D, B, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 594 | 0.72 | 0.80 | 34 | empty |
| 2 | 589 | 0.72 | 0.79 | 40 | empty |
| 3 | 74 | 0.51 | 0.84 | 21 | empty |
| 4 | 52 | 0.25 | 0.73 | 10 | empty |
Interfaces
7 interfaces between chains.
- A–D · 678 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 327 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 324 Ų buried · 5 hydrogen bonds · protein-protein
- E–F · 323 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 322 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7E1J · Crystal structure of Pr55Gag-matrix domain in complex with IP6 in space group C121 · 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 T2CJ20
- Elsewhere: RCSB PDB 7E1J · PDBe 7E1J · UniProt T2CJ20
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