Research workbench
Structure of HIV-1 capsid protein by cryo-EM
Analyse Structure of HIV-1 capsid protein by cryo-EM in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3J34
- Type
- protein
- Length
- 9,702 residues
- Chains
- 42
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein
- UniProt
- Q79791
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 1 distinct chain · 54% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, 5, a, b, c, 6, i, j, k, l, m, 7, d, e, f, g, h | Capsid protein | protein | 231 | 54% helix, 2% strand | Q79791 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1058 | 0.82 | 0.83 | 127 | empty |
| 2 | 1139 | 0.79 | 0.80 | 128 | empty |
| 3 | 652 | 0.77 | 0.82 | 80 | empty |
| 4 | 952 | 0.77 | 0.79 | 102 | empty |
| 5 | 1192 | 0.77 | 0.79 | 90 | empty |
Interfaces
83 interfaces between chains.
- I–J · 1645 Ų buried · 10 hydrogen bonds · protein-protein
- A–F · 1644 Ų buried · 12 hydrogen bonds · protein-protein
- G–H · 1626 Ų buried · 15 hydrogen bonds · protein-protein
- 5–a · 1618 Ų buried · 17 hydrogen bonds · protein-protein
- 7–h · 1582 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 disulfide (disulfide).
Compared structures
- 3J34 · Structure of HIV-1 Capsid Protein by Cryo-EM · the same entry in another collection · chain D against D, 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 Q79791
- Elsewhere: RCSB PDB 3J34 · PDBe 3J34 · UniProt Q79791
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