MolNFT v1 · #122810 · protein + DNA
Lambda excision hj intermediate
5J0N · Attp(-117 to +79): “Lambda excision hj intermediate”. Electron microscopy, 20 pockets (best druggability 0.84). MolNFT v1 #122810 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5J0N
- Type
- protein + DNA
- Length
- 2,349 residues
- Chains
- 15
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Attp(-117 to +79); Attb(-21) to ATTP(+117); Attb(-19 to +21); Attp(-79) to ATTB(+19)…
- EC
- 2.7.7.-, 3.1.-.-
- UniProt
- P03700, B7MAS3, B7MHM1, P03699
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 12 distinct chains · 40% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Attp(-117 to +79) | dna | 197 | — | — |
| B | Attb(-21) to ATTP(+117) | dna | 139 | — | — |
| C | Attb(-19 to +21) | dna | 41 | — | — |
| D | Attp(-79) to ATTB(+19) | dna | 99 | — | — |
| E | Integrase (EC 2.7.7.-, 3.1.-.-) | protein | 274 | 48% helix, 6% strand | P03700 |
| F, H | Integrase (EC 2.7.7.-, 3.1.-.-) | protein | 356 | 38% helix, 9% strand | P03700 |
| G | Integrase (EC 2.7.7.-, 3.1.-.-) | protein | 345 | 41% helix, 6% strand | P03700 |
| I, K | Integration host factor subunit alpha | protein | 96 | 39% helix, 23% strand | B7MAS3 |
| J, L | Integration host factor subunit beta | protein | 94 | 39% helix, 19% strand | B7MHM1 |
| M | Excisionase | protein | 53 | 26% helix, 19% strand | P03699 |
| N | Excisionase | protein | 54 | 28% helix, 19% strand | P03699 |
| O | Excisionase | protein | 55 | 25% helix, 22% strand | P03699 |
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 | 850 | 0.84 | 0.87 | 90 | empty |
| 2 | 1065 | 0.80 | 0.82 | 76 | empty |
| 3 | 572 | 0.78 | 0.85 | 56 | empty |
| 4 | 1156 | 0.77 | 0.79 | 73 | empty |
| 5 | 1026 | 0.74 | 0.77 | 105 | empty |
Interfaces
43 interfaces between chains.
- A–B · 5155 Ų buried · 242 hydrogen bonds · nucleic-nucleic
- A–D · 3487 Ų buried · 198 hydrogen bonds · nucleic-nucleic
- K–L · 2618 Ų buried · 25 hydrogen bonds · protein-protein
- I–J · 2590 Ų buried · 23 hydrogen bonds · protein-protein
- D–G · 1768 Ų buried · 34 hydrogen bonds · protein-nucleic
Compared structures
- 5J0N · Lambda excision HJ intermediate · the same entry in another collection · chain O against O, 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 P03700
- Every structure of UniProt B7MAS3
- Every structure of UniProt B7MHM1
- Every structure of UniProt P03699
- Elsewhere: RCSB PDB 5J0N · PDBe 5J0N · UniProt P03700 · UniProt B7MAS3 · UniProt B7MHM1 · UniProt P03699
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