MolNFT v1 · #145435 · protein
Structure of an engineered protein (NUDT16TI) in complex with 53BP1 tudor domains
6CO2 · NUDT16-tudor-interacting (NUDT16TI): “Structure of an engineered protein (NUDT16TI) in complex with 53BP1 tudor domains”. X-ray diffraction, 6 pockets (best druggability 0.71). MolNFT v1 #145435 on GenesisL1: 3D structure, binding…
- 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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