MolNFT v1 · #128846 · protein
Llama vhh in complex with P24
5O2U · Capsid protein P24: “Llama vhh in complex with P24”. X-ray diffraction, 2 pockets (best druggability 0.47). MolNFT v1 #128846 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5O2U
- Type
- protein
- Length
- 377 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein P24; Vhh 59H10
- UniProt
- P12493
- Pockets
- 2 · best druggability 0.47
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Capsid protein P24 | protein | 73 | 64% helix, 0% strand | P12493 |
| B | Vhh 59H10 | protein | 115 | 5% helix, 50% strand | — |
| D | Vhh 59H10 | protein | 116 | 5% helix, 49% strand | — |
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 176 | 0.47 | 0.75 | 24 | empty |
| 2 | 191 | 0.44 | 0.73 | 25 | empty |
Interfaces
3 interfaces between chains.
- C–D · 676 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 666 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 529 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5O2U · Llama VHH in complex with p24 · 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 P12493
- Elsewhere: RCSB PDB 5O2U · PDBe 5O2U · UniProt P12493
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