Research workbench
Microed structure of the ctd-SP1 fragment of HIV-1 gag
Analyse Microed structure of the ctd-SP1 fragment of HIV-1 gag in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6N3J
- Type
- protein
- Length
- 545 residues
- Chains
- 6
- Method
- electron crystallography
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ctd-SP1 fragment of HIV-1 gag
- UniProt
- A0A248SMC7
- Pockets
- 4 · best druggability 0.76
Structure
electron crystallography · 2 distinct chains · 67% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E, F | Ctd-SP1 fragment of HIV-1 gag | protein | 91 | 66% helix, 0% strand | A0A248SMC7 |
| D | Ctd-SP1 fragment of HIV-1 gag | protein | 90 | 68% helix, 0% strand | A0A248SMC7 |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 987 | 0.76 | 0.78 | 108 | empty |
| 2 | 119 | 0.50 | 0.80 | 29 | empty |
| 3 | 55 | 0.31 | 0.76 | 21 | empty |
| 4 | 54 | 0.29 | 0.75 | 18 | empty |
Interfaces
6 interfaces between chains.
- A–F · 696 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 678 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 676 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 661 Ų buried · 4 hydrogen bonds · protein-protein
- D–E · 647 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6N3J · MicroED Structure of the CTD-SP1 fragment of HIV-1 Gag · the same entry in another collection · chain B against B, 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 A0A248SMC7
- Elsewhere: RCSB PDB 6N3J · PDBe 6N3J · UniProt A0A248SMC7
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