MolNFT v1 · #136316 · protein
Structure of the HIV-1 capsid protein and spacer peptide 1 by cryo-EM
5UP4: “Structure of the HIV-1 capsid protein and spacer peptide 1 by cryo-EM”. Electron microscopy, 20 pockets (best druggability 0.77). MolNFT v1 #136316 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5UP4
- Type
- protein
- Length
- 3,978 residues
- Chains
- 18
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 capsid protein and spacer peptide 1
- UniProt
- B6DRA0
- Pockets
- 20 · best druggability 0.77
Structure
electron microscopy · 1 distinct chain · 61% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, K, L, M, N, O, P, Q, R, S, C, D, E, F, G, H, I, J | HIV-1 capsid protein and spacer peptide 1 | protein | 221 | 61% helix, 4% strand | B6DRA0 |
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 | 1013 | 0.77 | 0.79 | 113 | empty |
| 2 | 817 | 0.75 | 0.79 | 83 | empty |
| 3 | 686 | 0.73 | 0.79 | 69 | empty |
| 4 | 1141 | 0.73 | 0.76 | 100 | empty |
| 5 | 736 | 0.73 | 0.79 | 87 | empty |
Interfaces
24 interfaces between chains.
- O–Q · 1303 Ų buried · 8 hydrogen bonds · protein-protein
- H–J · 1276 Ų buried · 10 hydrogen bonds · protein-protein
- K–M · 1276 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 1275 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 1265 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide (disulfide).
Compared structures
- 5UP4 · Structure of the HIV-1 Capsid Protein and spacer peptide 1 by Cryo-EM · the same entry in another collection · chain P against P, 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 5UP4 · PDBe 5UP4 · UniProt B6DRA0
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