Research workbench
Structure of an engineered protein (NUDT16TI) in complex with 53BP1 tudor domains
Analyse Structure of an engineered protein (NUDT16TI) in complex with 53BP1 tudor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CO2
- Type
- protein
- Length
- 596 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NUDT16-tudor-interacting (NUDT16TI); TP53-binding protein 1
- EC
- 3.6.1.62, 3.6.1.64
- UniProt
- Q96DE0, Q12888
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | NUDT16-tudor-interacting (NUDT16TI) (EC 3.6.1.62, 3.6.1.64) | protein | 180 | 30% helix, 33% strand | Q96DE0 |
| C | TP53-binding protein 1 | protein | 118 | 13% helix, 52% strand | Q12888 |
| D | TP53-binding protein 1 | protein | 118 | 10% helix, 52% strand | Q12888 |
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 608 | 0.71 | 0.79 | 56 | empty |
| 2 | 67 | 0.70 | 0.96 | 17 | empty |
| 3 | 368 | 0.62 | 0.78 | 37 | empty |
| 4 | 304 | 0.55 | 0.75 | 36 | empty |
| 5 | 56 | 0.48 | 0.85 | 13 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1359 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 812 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 440 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 110 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6CO2 · Structure of an engineered protein (NUDT16TI) in complex with 53BP1 Tudor domains · the same entry in another collection · chain A against A, TM-score 1.00
- Q96DE0 · AlphaFold monomer V2.0 prediction for U8 snorna-decapping enzyme (Q96DE0) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q12888 · AlphaFold monomer V2.0 prediction for TP53-binding protein 1 (Q12888) · a predicted model of the same protein · chain D against A, TM-score 0.95
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 Q96DE0
- Every structure of UniProt Q12888
- Elsewhere: RCSB PDB 6CO2 · PDBe 6CO2 · UniProt Q96DE0 · UniProt Q12888
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