Research workbench
Nhej long-range synaptic complex
Analyse Nhej long-range synaptic complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LT3
- Type
- protein + DNA
- Length
- 11,423 residues
- Chains
- 20
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- X-ray repair cross-complementing protein 6; X-ray repair cross-complementing protein 5…
- EC
- 3.6.4.-, 4.2.99.-, 2.7.11.1, 6.5.1.1
- UniProt
- P12956, P13010, P78527, Q13426, Q9H9Q4, P49917
- Ligands
- ADP
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 11 distinct chains · 56% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, J | X-ray repair cross-complementing protein 6 (EC 3.6.4.-, 4.2.99.-) | protein | 497 | 30% helix, 22% strand | P12956 |
| B, K | X-ray repair cross-complementing protein 5 (EC 3.6.4.-) | protein | 531 | 32% helix, 22% strand | P13010 |
| C, L | DNA-dependent protein kinase catalytic subunit (EC 2.7.11.1) | protein | 3720 | 65% helix, 2% strand | P78527 |
| Q, R | Unknown peptide | protein | 20 | 55% helix, 0% strand | — |
| D, M | DNA (31-mer) | dna | 31 | — | — |
| E, N | DNA (30-mer) | dna | 30 | — | — |
| F, P | DNA repair protein XRCC4 | protein | 213 | 50% helix, 25% strand | Q13426 |
| G, O | DNA repair protein XRCC4 | protein | 195 | 53% helix, 29% strand | Q13426 |
| H | Non-homologous end-joining factor 1 | protein | 223 | 49% helix, 25% strand | Q9H9Q4 |
| I | Non-homologous end-joining factor 1 | protein | 218 | 47% helix, 25% strand | Q9H9Q4 |
| X, Y | DNA ligase 4 (EC 6.5.1.1) | protein | 254 | 41% helix, 12% strand | P49917 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains C, L
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 | 826 | 0.87 | 0.90 | 85 | empty |
| 2 | 860 | 0.85 | 0.87 | 98 | empty |
| 3 | 994 | 0.85 | 0.86 | 124 | empty |
| 4 | 774 | 0.85 | 0.88 | 92 | empty |
| 5 | 1012 | 0.84 | 0.85 | 121 | empty |
Interfaces
43 interfaces between chains.
- J–K · 9172 Ų buried · 99 hydrogen bonds · protein-protein
- A–B · 9152 Ų buried · 98 hydrogen bonds · protein-protein
- H–I · 3277 Ų buried · 31 hydrogen bonds · protein-protein
- O–P · 2813 Ų buried · 18 hydrogen bonds · protein-protein
- F–G · 2812 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 7LT3 · NHEJ Long-range synaptic complex · the same entry in another collection · chain K against K, 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 P12956
- Every structure of UniProt P13010
- Every structure of UniProt P78527
- Every structure of UniProt Q13426
- Every structure of UniProt Q9H9Q4
- Every structure of UniProt P49917
- Elsewhere: RCSB PDB 7LT3 · PDBe 7LT3 · UniProt P12956 · UniProt P13010 · UniProt P78527 · UniProt Q13426 · UniProt Q9H9Q4 · UniProt P49917
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