Research workbench
Two domain fragment of HIV-2 integrase in complex with ledgf ibd
Analyse Two domain fragment of HIV-2 integrase in complex with ledgf ibd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3F9K
- Type
- protein
- Length
- 5,928 residues
- Chains
- 36
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrase; PC4 and SFRS1-interacting protein
- UniProt
- P04584, O75475
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, I, M, Q, U, Y, c, g, k, o, s | Integrase | protein | 204 | 45% helix, 17% strand | P04584 |
| B, F, J, N, R, V, Z, d, h, l, p, t | Integrase | protein | 196 | 49% helix, 17% strand | P04584 |
| C, G, K, O, S, W, a, e, i, m, q, u | PC4 and SFRS1-interacting protein | protein | 94 | 71% helix, 4% strand | O75475 |
Ligands and binding sites
- ZN · Zinc ion · metal · 24 copies · chains A, B, E, F, I, J, M, N, Q, R, U, V, Y, Z, c, d, g, h, k, l, o, p, s, t
- MG · Magnesium ion · metal · 24 copies · chains A, B, E, F, I, J, M, N, Q, R, U, V, Y, Z, c, d, g, h, k, l, o, p, s, t
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 917 | 0.86 | 0.87 | 137 | empty |
| 2 | 638 | 0.83 | 0.87 | 81 | empty |
| 3 | 568 | 0.82 | 0.87 | 80 | empty |
| 4 | 581 | 0.82 | 0.87 | 74 | empty |
| 5 | 447 | 0.82 | 0.89 | 45 | empty |
Interfaces
101 interfaces between chains.
- I–J · 1539 Ų buried · 28 hydrogen bonds · protein-protein
- s–t · 1537 Ų buried · 28 hydrogen bonds · protein-protein
- Y–Z · 1537 Ų buried · 28 hydrogen bonds · protein-protein
- U–V · 1536 Ų buried · 26 hydrogen bonds · protein-protein
- M–N · 1535 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 3F9K · Two domain fragment of HIV-2 integrase in complex with LEDGF IBD · 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 P04584
- Every structure of UniProt O75475
- Elsewhere: RCSB PDB 3F9K · PDBe 3F9K · UniProt P04584 · UniProt O75475
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