MolNFT v1 · #164270 · protein
Human endogenous retrovirus (HML2) mature capsid assembly, T=3 icosahedron
6SSM · Endogenous retrovirus group K member 24 gag polyprotein: “Human endogenous retrovirus (HML2) mature capsid assembly, T=3 icosahedron”. Electron microscopy, 13 pockets (best druggability 0.73). MolNFT v1 #164270 on GenesisL1: 3D…
- PDB
- 6SSM
- Type
- protein
- Length
- 654 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endogenous retrovirus group K member 24 gag polyprotein
- UniProt
- P63145
- Pockets
- 13 · best druggability 0.73
Structure
electron microscopy · 1 distinct chain · 58% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, B | Endogenous retrovirus group K member 24 gag polyprotein | protein | 218 | 58% helix, 0% strand | P63145 |
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 756 | 0.73 | 0.78 | 89 | empty |
| 2 | 66 | 0.71 | 0.96 | 20 | empty |
| 3 | 68 | 0.70 | 0.95 | 15 | empty |
| 4 | 61 | 0.64 | 0.93 | 20 | empty |
| 5 | 66 | 0.63 | 0.91 | 17 | empty |
Interfaces
2 interfaces between chains.
- A–B · 718 Ų buried · 1 hydrogen bond · protein-protein
- C–B · 402 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6SSM · Human endogenous retrovirus (HML2) mature capsid assembly, T=3 icosahedron · the same entry in another collection · chain A against A, TM-score 1.00
- P63145 · AlphaFold monomer V2.0 prediction for endogenous retrovirus group K member 24 gag… · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P63145
- Elsewhere: RCSB PDB 6SSM · PDBe 6SSM · UniProt P63145
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