Research workbench
Structure of HIV cleaved synaptic complex (csc) intasome bound with calcium
Analyse Structure of HIV cleaved synaptic complex (csc) intasome bound with calcium in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PUT
- Type
- protein + DNA
- Length
- 619 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chimeric SSO7D and HIV-1 integrase; Viral DNA transferred strand; Viral DNA…
- UniProt
- P39476, Q76353
- Ligands
- CA, ZN
- Pockets
- 10 · best druggability 0.66
Structure
electron microscopy · 6 distinct chains · 41% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chimeric SSO7D and HIV-1 integrase | protein | 244 | 48% helix, 15% strand | P39476, Q76353 |
| B | Chimeric SSO7D and HIV-1 integrase | protein | 231 | 48% helix, 21% strand | P39476, Q76353 |
| C | Chimeric SSO7D and HIV-1 integrase | protein | 63 | 17% helix, 46% strand | P39476, Q76353 |
| D | Chimeric SSO7D and HIV-1 integrase | protein | 47 | 6% helix, 60% strand | P39476, Q76353 |
| F | Viral DNA transferred strand | dna | 16 | — | — |
| E | Viral DNA non-transferred strand | dna | 18 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 537 | 0.66 | 0.78 | 47 | empty |
| 2 | 387 | 0.61 | 0.77 | 53 | empty |
| 3 | 112 | 0.52 | 0.82 | 19 | empty |
| 4 | 135 | 0.50 | 0.79 | 20 | empty |
| 5 | 234 | 0.50 | 0.75 | 22 | empty |
Interfaces
11 interfaces between chains.
- A–B · 1644 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1627 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 800 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 752 Ų buried · 15 hydrogen bonds · protein-nucleic
- F–E · 665 Ų buried · 42 hydrogen bonds · nucleic-nucleic
Compared structures
- 6PUT · Structure of HIV cleaved synaptic complex (CSC) intasome bound with calcium · the same entry in another collection · chain E against E, TM-score 1.00
- P39476 · AlphaFold monomer V2.0 prediction for DNA-binding protein 7D (P39476) · a predicted model of the same protein · chain D against A, TM-score 0.51
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 P39476
- Every structure of UniProt Q76353
- Elsewhere: RCSB PDB 6PUT · PDBe 6PUT · UniProt P39476 · UniProt Q76353
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