MolNFT v1 · #126361 · protein + DNA
Cryo-EM reconstruction of the maedi-visna virus (mvv) strand transfer complex
5M0R · Integrase: “Cryo-EM reconstruction of the maedi-visna virus (mvv) strand transfer complex”. Electron microscopy, 20 pockets (best druggability 0.83). MolNFT v1 #126361 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5M0R
- Type
- protein + DNA
- Length
- 4,064 residues
- Chains
- 22
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrase; Vdna, non-transfered strand; Vdna-tdna, transferred strand, joined to a model…
- 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 0.83
Structure
electron microscopy · 11 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 | 276 | 42% helix, 19% 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, 22% 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, 22% 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 | 43% helix, 25% strand | P35956 |
| E, 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 | 257 | 47% helix, 21% strand | P35956 |
| F, 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 | 266 | 47% helix, 20% 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 | 60% helix, 15% 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, 27% strand | P35956 |
| Q, S | Vdna, non-transfered strand | dna | 21 | — | — |
| R, T | Vdna-tdna, transferred strand, joined to a model tdna | dna | 41 | — | — |
| U, V | Tdna | dna | 16 | — | — |
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 | 1008 | 0.83 | 0.84 | 109 | empty |
| 2 | 994 | 0.82 | 0.83 | 108 | empty |
| 3 | 701 | 0.81 | 0.85 | 72 | empty |
| 4 | 1039 | 0.80 | 0.82 | 93 | empty |
| 5 | 128 | 0.80 | 0.97 | 25 | empty |
Interfaces
80 interfaces between chains.
- N–O · 1700 Ų buried · 13 hydrogen bonds · protein-protein
- F–G · 1681 Ų buried · 9 hydrogen bonds · protein-protein
- G–H · 1566 Ų buried · 7 hydrogen bonds · protein-protein
- M–P · 1551 Ų buried · 25 hydrogen bonds · protein-protein
- E–H · 1551 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 5M0R · Cryo-EM reconstruction of the maedi-visna virus (MVV) strand transfer complex · 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 P35956
- Elsewhere: RCSB PDB 5M0R · PDBe 5M0R · UniProt P35956
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