MolNFT v1 · #135516 · protein + DNA
Structure of tetrameric HIV-1 strand transfer complex intasome
5U1C · HIV-1 integrase, SSO7D chimera: “Structure of tetrameric HIV-1 strand transfer complex intasome”. Electron microscopy, 2 ligands (ZN, MG), 20 pockets (best druggability 0.73). MolNFT v1 #135516 on GenesisL1: 3D structure, binding…
- PDB
- 5U1C
- Type
- protein + DNA
- Length
- 940 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 integrase, SSO7D chimera; DNA (11-mer); DNA (23-mer); DNA (37-mer)
- UniProt
- A0A157T5S7, F2WR39
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.73
Structure
electron microscopy · 5 distinct chains · 41% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | HIV-1 integrase, SSO7D chimera | protein | 251 | 41% helix, 22% strand | A0A157T5S7, F2WR39 |
| B, D | HIV-1 integrase, SSO7D chimera | protein | 172 | 40% helix, 28% strand | A0A157T5S7, F2WR39 |
| G, H | DNA (11-mer) | dna | 8 | — | — |
| E, I | DNA (23-mer) | dna | 14 | — | — |
| F, J | DNA (37-mer) | dna | 25 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, C
- MG · Magnesium ion · metal · 2 copies · chains A, G, J, F, C, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 368 | 0.73 | 0.85 | 58 | empty |
| 2 | 284 | 0.71 | 0.85 | 46 | empty |
| 3 | 210 | 0.62 | 0.82 | 27 | empty |
| 4 | 204 | 0.62 | 0.82 | 20 | empty |
| 5 | 137 | 0.59 | 0.84 | 19 | empty |
Interfaces
26 interfaces between chains.
- C–D · 2076 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 2069 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 1148 Ų buried · 18 hydrogen bonds · protein-protein
- E–C · 1002 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–I · 999 Ų buried · 18 hydrogen bonds · protein-nucleic
Compared structures
- 5U1C · Structure of tetrameric HIV-1 Strand Transfer Complex Intasome · 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 A0A157T5S7
- Every structure of UniProt F2WR39
- Elsewhere: RCSB PDB 5U1C · PDBe 5U1C · UniProt A0A157T5S7 · UniProt F2WR39
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