MolNFT v1 · #172501 · protein
Envelope glycprotein of endogenous retrovirus Y032 (atlas virus) from the human hookworm ancylostoma ceylanicum
7A4A · Integrase catalytic domain-containing protein: “Envelope glycprotein of endogenous retrovirus Y032 (atlas virus) from the human hookworm ancylostoma…”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.87). MolNFT…
- 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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