MolNFT v1 · #57023 · protein
Crystal structure of CDT1/GEMININ complex
2ZXX: “Crystal structure of CDT1/GEMININ complex”. X-ray diffraction, 5 pockets (best druggability 0.74). MolNFT v1 #57023 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2ZXX
- Type
- protein
- Length
- 660 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Geminin; DNA replication factor CDT1
- UniProt
- O88513, Q8R4E9
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 61% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Geminin | protein | 70 | 83% helix, 0% strand | O88513 |
| B, E | Geminin | protein | 78 | 79% helix, 0% strand | O88513 |
| C | DNA replication factor CDT1 | protein | 185 | 49% helix, 8% strand | Q8R4E9 |
| D | Geminin | protein | 65 | 88% helix, 0% strand | O88513 |
| F | DNA replication factor CDT1 | protein | 184 | 47% helix, 8% strand | Q8R4E9 |
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 872 | 0.74 | 0.78 | 69 | empty |
| 2 | 654 | 0.70 | 0.78 | 46 | empty |
| 3 | 151 | 0.68 | 0.89 | 35 | empty |
| 4 | 131 | 0.63 | 0.86 | 28 | empty |
| 5 | 54 | 0.25 | 0.73 | 16 | empty |
Interfaces
13 interfaces between chains.
- A–B · 1565 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 1480 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 968 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 937 Ų buried · 9 hydrogen bonds · protein-protein
- B–F · 446 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 2ZXX · Crystal structure of Cdt1/geminin complex · the same entry in another collection · chain F against F, TM-score 1.00
- Q8R4E9 · AlphaFold monomer V2.0 prediction for DNA replication factor CDT1 (Q8R4E9) · a predicted model of the same protein · chain F against A, TM-score 0.99
- O88513 · AlphaFold monomer V2.0 prediction for geminin (O88513) · a predicted model of the same protein · chain E against A, TM-score 0.87
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 O88513
- Every structure of UniProt Q8R4E9
- Elsewhere: RCSB PDB 2ZXX · PDBe 2ZXX · UniProt O88513 · UniProt Q8R4E9
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