Research workbench
Cryo-EM structure of nhej super-complex (monomer)
Analyse Cryo-EM structure of nhej super-complex (monomer) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NFE
- Type
- protein + DNA
- Length
- 5,660 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-dependent protein kinase catalytic SUBUNIT,DNA- dependent protein kinase catalytic…
- EC
- 2.7.11.1, 3.6.4.-, 4.2.99.-, 6.5.1.1
- UniProt
- P78527, P12956, P13010, Q9H9Q4, Q13426, P49917
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 10 distinct chains · 55% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-dependent protein kinase catalytic SUBUNIT,DNA- dependent protein kinase catalytic SUBUNIT,DNA-dependent protein kinase catalytic subunit (EC 2.7.11.1) | protein | 3585 | 66% helix, 2% strand | P78527 |
| B | X-ray repair cross-complementing protein 6 (EC 3.6.4.-, 4.2.99.-) | protein | 475 | 27% helix, 23% strand | P12956 |
| C | X-ray repair cross-complementing protein 5 (EC 3.6.4.-) | protein | 513 | 32% helix, 21% strand | P13010 |
| F | Non-homologous end-joining factor 1 | protein | 190 | 37% helix, 1% strand | Q9H9Q4 |
| G | Non-homologous end-joining factor 1 | protein | 197 | 35% helix, 8% strand | Q9H9Q4 |
| H | DNA repair protein XRCC4 | protein | 201 | 50% helix, 11% strand | Q13426 |
| I | DNA repair protein XRCC4 | protein | 193 | 51% helix, 15% strand | Q13426 |
| J | DNA ligase 4 (EC 6.5.1.1) | protein | 258 | 31% helix, 12% strand | P49917 |
| D | DNA (5'- D(P*AP*AP*TP*AP*AP*AP*CP*TP*AP*AP*AP*AP*AP*CP*TP*AP*TP*TP*AP*TP*TP*AP *TP*G)-3') | dna | 24 | — | — |
| E | DNA (5'- D(P*TP*AP*AP*TP*AP*AP*TP*AP*GP*TP*TP*TP*TP*TP*AP*GP*TP*TP*TP*AP*TP*TP *AP*G)-3') | dna | 24 | — | — |
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 | 1109 | 0.85 | 0.86 | 122 | empty |
| 2 | 584 | 0.84 | 0.90 | 88 | empty |
| 3 | 578 | 0.83 | 0.89 | 78 | empty |
| 4 | 957 | 0.82 | 0.83 | 106 | empty |
| 5 | 198 | 0.81 | 0.95 | 26 | empty |
Interfaces
19 interfaces between chains.
- B–C · 8365 Ų buried · 108 hydrogen bonds · protein-protein
- F–G · 2913 Ų buried · 20 hydrogen bonds · protein-protein
- H–I · 2634 Ų buried · 19 hydrogen bonds · protein-protein
- I–J · 1411 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1319 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 7NFE · Cryo-EM structure of NHEJ super-complex (monomer) · the same entry in another collection · chain E against E, TM-score 1.00
- Q13426 · AlphaFold monomer V2.0 prediction for DNA repair protein XRCC4 (Q13426) · a predicted model of the same protein · chain I against A, TM-score 0.86
- P13010 · AlphaFold monomer V2.0 prediction for X-ray repair cross- complementing protein 5 (P13010) · a predicted model of the same protein · chain C against A, TM-score 0.81
- Q9H9Q4 · AlphaFold monomer V2.0 prediction for non-homologous end-joining factor 1 (Q9H9Q4) · a predicted model of the same protein · chain G against A, TM-score 0.78
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 P78527
- Every structure of UniProt P12956
- Every structure of UniProt P13010
- Every structure of UniProt Q9H9Q4
- Every structure of UniProt Q13426
- Every structure of UniProt P49917
- Elsewhere: RCSB PDB 7NFE · PDBe 7NFE · UniProt P78527 · UniProt P12956 · UniProt P13010 · UniProt Q9H9Q4 · UniProt Q13426 · UniProt P49917
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