Research workbench
DNA binding domain of NDC10
Analyse DNA binding domain of NDC10 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SQI
- Type
- protein + DNA
- Length
- 418 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- KLLA0E03807P; DNA (5'-D(P*TP*TP*AP*AP*TP*TP*TP*AP*TP*AP*AP*AP*AP*TP*T)- 3'); DNA…
- UniProt
- Q6CPM4
- Pockets
- 7 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | KLLA0E03807P | protein | 388 | 52% helix, 6% strand | Q6CPM4 |
| B | DNA (5'-D(P*TP*TP*AP*AP*TP*TP*TP*AP*TP*AP*AP*AP*AP*TP*T)- 3') | dna | 15 | — | — |
| C | DNA (5'-D(P*AP*AP*AP*TP*TP*TP*TP*AP*TP*AP*AP*AP*TP*TP*A)- 3') | dna | 15 | — | — |
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 369 | 0.64 | 0.79 | 33 | empty |
| 2 | 106 | 0.50 | 0.81 | 17 | empty |
| 3 | 214 | 0.48 | 0.75 | 25 | empty |
| 4 | 157 | 0.44 | 0.75 | 26 | empty |
| 5 | 107 | 0.40 | 0.76 | 19 | empty |
Interfaces
3 interfaces between chains.
- B–C · 636 Ų buried · 50 hydrogen bonds · nucleic-nucleic
- A–C · 382 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–B · 345 Ų buried · 2 hydrogen bonds · protein-nucleic
Compared structures
- 3SQI · DNA binding domain of Ndc10 · 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 Q6CPM4
- Elsewhere: RCSB PDB 3SQI · PDBe 3SQI · UniProt Q6CPM4
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