Research workbench
Ca-targeting nanobody is a tool for studying HIV-1 capsid lattice interactions
Analyse Ca-targeting nanobody is a tool for studying HIV-1 capsid lattice interactions in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7N9U
- Type
- protein
- Length
- 992 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein; Nanobody
- UniProt
- B6DRA0
- Pockets
- 9 · best druggability 0.68
Structure
x-ray diffraction · 5 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein | protein | 214 | 59% helix, 3% strand | B6DRA0 |
| B | Capsid protein | protein | 214 | 60% helix, 3% strand | B6DRA0 |
| C | Capsid protein | protein | 219 | 59% helix, 3% strand | B6DRA0 |
| D, E | Nanobody | protein | 116 | 5% helix, 51% strand | — |
| F | Nanobody | protein | 113 | 5% helix, 53% strand | — |
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 374 | 0.68 | 0.81 | 61 | empty |
| 2 | 310 | 0.65 | 0.81 | 48 | empty |
| 3 | 316 | 0.55 | 0.75 | 44 | empty |
| 4 | 95 | 0.51 | 0.82 | 19 | empty |
| 5 | 89 | 0.49 | 0.82 | 21 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1237 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1138 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 707 Ų buried · 11 hydrogen bonds · protein-protein
- B–F · 662 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 660 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7N9U · CA-targeting nanobody is a tool for studying HIV-1 capsid lattice interactions · 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 B6DRA0
- Elsewhere: RCSB PDB 7N9U · PDBe 7N9U · UniProt B6DRA0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.