Research workbench
Complex of aplf factor and ku heterodimer bound to DNA
Analyse Complex of aplf factor and ku heterodimer bound to DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ERF
- Type
- protein + DNA
- Length
- 4,233 residues
- Chains
- 20
- Method
- x-ray diffraction
- 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.-, 4.2.99.18
- UniProt
- P12956, P13010, Q8IW19
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 15 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | X-ray repair cross-complementing protein 6 (EC 3.6.4.-, 4.2.99.-) | protein | 493 | 31% helix, 25% strand | P12956 |
| B | X-ray repair cross-complementing protein 5 (EC 3.6.4.-) | protein | 521 | 33% helix, 27% strand | P13010 |
| C | X-ray repair cross-complementing protein 6 (EC 3.6.4.-, 4.2.99.-) | protein | 500 | 31% helix, 25% strand | P12956 |
| D | X-ray repair cross-complementing protein 5 (EC 3.6.4.-) | protein | 520 | 33% helix, 27% strand | P13010 |
| E | X-ray repair cross-complementing protein 6 (EC 3.6.4.-, 4.2.99.-) | protein | 497 | 31% helix, 25% strand | P12956 |
| F, H | X-ray repair cross-complementing protein 5 (EC 3.6.4.-) | protein | 526 | 32% helix, 27% strand | P13010 |
| G | X-ray repair cross-complementing protein 6 (EC 3.6.4.-, 4.2.99.-) | protein | 495 | 31% helix, 25% strand | P12956 |
| I, O | DNA (5'- D(*GP*TP*TP*TP*TP*TP*AP*GP*TP*TP*TP*AP*TP*TP*GP*GP*GP*CP*GP*CP*G)- 3') | dna | 14 | — | — |
| J | DNA (34-mer) | dna | 12 | — | — |
| K, M | DNA (5'- D(*GP*TP*TP*TP*TP*TP*AP*GP*TP*TP*TP*AP*TP*TP*GP*GP*GP*CP*GP*CP*G)- 3') | dna | 13 | — | — |
| L | DNA (34-mer) | dna | 10 | — | — |
| N | DNA (34-mer) | dna | 14 | — | — |
| P | DNA (34-mer) | dna | 16 | — | — |
| Q, S, T | Aprataxin and pnk-like factor (EC 4.2.99.18) | protein | 12 | 0% helix, 0% strand | Q8IW19 |
| R | Aprataxin and pnk-like factor (EC 4.2.99.18) | protein | 13 | 0% helix, 0% strand | Q8IW19 |
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 | 1136 | 0.87 | 0.88 | 102 | empty |
| 2 | 617 | 0.85 | 0.90 | 75 | empty |
| 3 | 635 | 0.85 | 0.90 | 72 | empty |
| 4 | 563 | 0.85 | 0.91 | 61 | empty |
| 5 | 466 | 0.80 | 0.87 | 50 | empty |
Interfaces
39 interfaces between chains.
- C–D · 9952 Ų buried · 117 hydrogen bonds · protein-protein
- E–F · 9859 Ų buried · 112 hydrogen bonds · protein-protein
- G–H · 9813 Ų buried · 117 hydrogen bonds · protein-protein
- A–B · 9767 Ų buried · 119 hydrogen bonds · protein-protein
- H–T · 743 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 6ERF · Complex of APLF factor and Ku heterodimer bound to DNA · 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 Q8IW19
- Elsewhere: RCSB PDB 6ERF · PDBe 6ERF · UniProt P12956 · UniProt P13010 · UniProt Q8IW19
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