Research workbench
Microed structure of the ctd-SP1 fragment of HIV-1 gag with bound maturation inhibitor bevirimat.
Analyse Microed structure of the ctd-SP1 fragment of HIV-1 gag with bound maturation… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6N3U
- Type
- protein
- Length
- 549 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
- 6 · best druggability 0.79
Structure
electron crystallography · 3 distinct chains · 66% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E | Ctd-SP1 fragment of HIV-1 gag | protein | 91 | 66% helix, 0% strand | A0A248SMC7 |
| B | Ctd-SP1 fragment of HIV-1 gag | protein | 92 | 66% helix, 0% strand | A0A248SMC7 |
| C, F | Ctd-SP1 fragment of HIV-1 gag | protein | 92 | 65% helix, 0% strand | A0A248SMC7 |
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1066 | 0.79 | 0.80 | 92 | empty |
| 2 | 86 | 0.50 | 0.83 | 26 | empty |
| 3 | 52 | 0.39 | 0.81 | 15 | empty |
| 4 | 78 | 0.35 | 0.76 | 22 | empty |
| 5 | 52 | 0.28 | 0.74 | 16 | empty |
Interfaces
6 interfaces between chains.
- D–E · 770 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 759 Ų buried · 4 hydrogen bonds · protein-protein
- A–F · 752 Ų buried · 5 hydrogen bonds · protein-protein
- E–F · 745 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 699 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6N3U · MicroED Structure of the CTD-SP1 fragment of HIV-1 Gag with bound maturation inhibitor… · 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 A0A248SMC7
- Elsewhere: RCSB PDB 6N3U · PDBe 6N3U · UniProt A0A248SMC7
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