Research workbench
Envelope glycprotein of endogenous retrovirus Y032 (atlas virus) from the human hookworm ancylostoma ceylanicum
Analyse Envelope glycprotein of endogenous retrovirus Y032 (atlas virus) from the human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7A4A
- Type
- protein
- Length
- 1,317 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrase catalytic domain-containing protein
- UniProt
- A0A016UZK2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 1 distinct chain · 3% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Integrase catalytic domain-containing protein | protein | 439 | 3% helix, 44% strand | A0A016UZK2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 798 | 0.87 | 0.89 | 103 | empty |
| 2 | 735 | 0.84 | 0.87 | 76 | empty |
| 3 | 147 | 0.80 | 0.97 | 33 | empty |
| 4 | 178 | 0.79 | 0.94 | 33 | empty |
| 5 | 97 | 0.77 | 0.98 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–C · 3201 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 3186 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 3186 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 45 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 7A4A · Envelope glycprotein of endogenous retrovirus Y032 (Atlas virus) from the human hookworm… · 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 A0A016UZK2
- Elsewhere: RCSB PDB 7A4A · PDBe 7A4A · UniProt A0A016UZK2
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