Research workbench
Human endogenous retrovirus (HML2) mature capsid assembly, D5 capsule
Analyse Human endogenous retrovirus (HML2) mature capsid assembly, D5 capsule in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SSK
- Type
- protein
- Length
- 1,987 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 0.74
Structure
electron microscopy · 7 distinct chains · 55% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endogenous retrovirus group K member 24 gag polyprotein | protein | 221 | 56% helix, 4% strand | P63145 |
| B | Endogenous retrovirus group K member 24 gag polyprotein | protein | 223 | 53% helix, 4% strand | P63145 |
| C | Endogenous retrovirus group K member 24 gag polyprotein | protein | 216 | 55% helix, 4% strand | P63145 |
| D, E, G | Endogenous retrovirus group K member 24 gag polyprotein | protein | 222 | 55% helix, 4% strand | P63145 |
| F | Endogenous retrovirus group K member 24 gag polyprotein | protein | 221 | 57% helix, 3% strand | P63145 |
| H | Endogenous retrovirus group K member 24 gag polyprotein | protein | 220 | 56% helix, 2% strand | P63145 |
| I | Endogenous retrovirus group K member 24 gag polyprotein | protein | 220 | 55% helix, 2% strand | P63145 |
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 927 | 0.74 | 0.77 | 97 | empty |
| 2 | 938 | 0.74 | 0.77 | 74 | empty |
| 3 | 799 | 0.72 | 0.77 | 68 | empty |
| 4 | 825 | 0.71 | 0.76 | 76 | empty |
| 5 | 733 | 0.69 | 0.76 | 71 | empty |
Interfaces
12 interfaces between chains.
- A–C · 1252 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 1067 Ų buried · 1 hydrogen bond · protein-protein
- D–F · 1056 Ų buried · 6 hydrogen bonds · protein-protein
- E–G · 1030 Ų buried · 4 hydrogen bonds · protein-protein
- F–H · 1029 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 6SSK · Human endogenous retrovirus (HML2) mature capsid assembly, D5 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 6SSK · PDBe 6SSK · UniProt P63145
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