MolNFT v1 · #126360 · protein + DNA
Cryo-EM reconstruction of the maedi-visna virus (mvv) intasome
5M0Q · Integrase: “Cryo-EM reconstruction of the maedi-visna virus (mvv) intasome”. Electron microscopy, 20 pockets (best druggability 0.85). MolNFT v1 #126360 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5M0Q
- Type
- protein + DNA
- Length
- 3,983 residues
- Chains
- 20
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrase; Vdna, non-transferred strand; Vdna, transferred strand
- EC
- 3.4.23.-, 2.7.7.49, 3.1.26.13, 3.1.13.2, 3.6.1.23, 2.7.7.-, 3.1.-.-
- UniProt
- P35956
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 12 distinct chains · 46% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, I | Integrase (EC 3.4.23.-, 2.7.7.49, 3.1.26.13, 3.1.13.2, 3.6.1.23, 2.7.7.-, 3.1.-.-) | protein | 275 | 41% helix, 20% strand | P35956 |
| B, J | Integrase (EC 3.4.23.-, 2.7.7.49, 3.1.26.13, 3.1.13.2, 3.6.1.23, 2.7.7.-, 3.1.-.-) | protein | 256 | 46% helix, 16% strand | P35956 |
| C, K | Integrase (EC 3.4.23.-, 2.7.7.49, 3.1.26.13, 3.1.13.2, 3.6.1.23, 2.7.7.-, 3.1.-.-) | protein | 261 | 49% helix, 23% strand | P35956 |
| D, L | Integrase (EC 3.4.23.-, 2.7.7.49, 3.1.26.13, 3.1.13.2, 3.6.1.23, 2.7.7.-, 3.1.-.-) | protein | 216 | 42% helix, 25% strand | P35956 |
| E | Integrase (EC 3.4.23.-, 2.7.7.49, 3.1.26.13, 3.1.13.2, 3.6.1.23, 2.7.7.-, 3.1.-.-) | protein | 257 | 46% helix, 22% strand | P35956 |
| F | Integrase (EC 3.4.23.-, 2.7.7.49, 3.1.26.13, 3.1.13.2, 3.6.1.23, 2.7.7.-, 3.1.-.-) | protein | 266 | 46% helix, 21% strand | P35956 |
| G, O | Integrase (EC 3.4.23.-, 2.7.7.49, 3.1.26.13, 3.1.13.2, 3.6.1.23, 2.7.7.-, 3.1.-.-) | protein | 205 | 59% helix, 16% strand | P35956 |
| H, P | Integrase (EC 3.4.23.-, 2.7.7.49, 3.1.26.13, 3.1.13.2, 3.6.1.23, 2.7.7.-, 3.1.-.-) | protein | 217 | 40% helix, 26% strand | P35956 |
| M | Integrase (EC 3.4.23.-, 2.7.7.49, 3.1.26.13, 3.1.13.2, 3.6.1.23, 2.7.7.-, 3.1.-.-) | protein | 256 | 48% helix, 20% strand | P35956 |
| N | Integrase (EC 3.4.23.-, 2.7.7.49, 3.1.26.13, 3.1.13.2, 3.6.1.23, 2.7.7.-, 3.1.-.-) | protein | 264 | 47% helix, 20% strand | P35956 |
| Q, S | Vdna, non-transferred strand | dna | 21 | — | — |
| R, T | Vdna, transferred strand | dna | 19 | — | — |
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 | 974 | 0.85 | 0.87 | 89 | empty |
| 2 | 729 | 0.84 | 0.88 | 86 | empty |
| 3 | 1057 | 0.83 | 0.83 | 116 | empty |
| 4 | 933 | 0.82 | 0.83 | 113 | empty |
| 5 | 379 | 0.81 | 0.90 | 63 | empty |
Interfaces
70 interfaces between chains.
- N–O · 1713 Ų buried · 13 hydrogen bonds · protein-protein
- F–G · 1657 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1611 Ų buried · 6 hydrogen bonds · protein-protein
- G–H · 1601 Ų buried · 10 hydrogen bonds · protein-protein
- K–L · 1582 Ų buried · 8 hydrogen bonds · protein-protein
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 P35956
- Elsewhere: RCSB PDB 5M0Q · PDBe 5M0Q · UniProt P35956
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