Research workbench
Human endogenous retrovirus (HML2) mature capsid assembly, D6 capsule
Analyse Human endogenous retrovirus (HML2) mature capsid assembly, D6 capsule in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SSL
- Type
- protein
- Length
- 1,973 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endogenous retrovirus group K member 24 gag polyprotein
- UniProt
- P63145
- Pockets
- 20 · best druggability 0.77
Structure
electron microscopy · 6 distinct chains · 54% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endogenous retrovirus group K member 24 gag polyprotein | protein | 219 | 54% helix, 1% strand | P63145 |
| B | Endogenous retrovirus group K member 24 gag polyprotein | protein | 219 | 57% helix, 1% strand | P63145 |
| C | Endogenous retrovirus group K member 24 gag polyprotein | protein | 213 | 53% helix, 0% strand | P63145 |
| D, E, I | Endogenous retrovirus group K member 24 gag polyprotein | protein | 220 | 49% helix, 0% strand | P63145 |
| F | Endogenous retrovirus group K member 24 gag polyprotein | protein | 222 | 54% helix, 2% strand | P63145 |
| G, H | Endogenous retrovirus group K member 24 gag polyprotein | protein | 220 | 55% helix, 1% strand | P63145 |
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1105 | 0.77 | 0.79 | 120 | empty |
| 2 | 1036 | 0.75 | 0.78 | 93 | empty |
| 3 | 993 | 0.74 | 0.77 | 95 | empty |
| 4 | 628 | 0.71 | 0.79 | 81 | empty |
| 5 | 754 | 0.70 | 0.77 | 67 | empty |
Interfaces
11 interfaces between chains.
- F–H · 1043 Ų buried · 4 hydrogen bonds · protein-protein
- E–G · 1011 Ų buried · 3 hydrogen bonds · protein-protein
- D–F · 1002 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 988 Ų buried · 2 hydrogen bonds · protein-protein
- G–H · 987 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6SSL · Human endogenous retrovirus (HML2) mature capsid assembly, D6 capsule · the same entry in another collection · chain I against I, 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 0.98
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 6SSL · PDBe 6SSL · UniProt P63145
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