MolNFT v1 · #58338 · protein
Crystal structure of the chicken cenp-T histone FOLD/CENP-W complex, crystal form II
3B0D · Centromere protein T: “Crystal structure of the chicken cenp-T histone FOLD/CENP-W complex, crystal form II”. X-ray diffraction, 3 pockets (best druggability 0.40). MolNFT v1 #58338 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3B0D
- Type
- protein
- Length
- 342 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Centromere protein T; Centromere protein W
- UniProt
- F1NPG5
- Pockets
- 3 · best druggability 0.40
Structure
x-ray diffraction · 3 distinct chains · 68% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | Centromere protein T | protein | 97 | 67% helix, 3% strand | F1NPG5 |
| W, C | Centromere protein W | protein | 75 | 69% helix, 4% strand | — |
| B | Centromere protein T | protein | 95 | 68% helix, 3% strand | F1NPG5 |
Ligands and binding sites
- CIT · Citric acid · additive · 4 copies · chains T, W, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 98 | 0.40 | 0.76 | 22 | empty |
| 2 | 60 | 0.39 | 0.80 | 15 | empty |
| 3 | 65 | 0.38 | 0.79 | 15 | empty |
Interfaces
5 interfaces between chains.
- B–C · 2640 Ų buried · 23 hydrogen bonds · protein-protein
- T–W · 2614 Ų buried · 25 hydrogen bonds · protein-protein
- T–B · 502 Ų buried · 3 hydrogen bonds · protein-protein
- W–B · 38 Ų buried · 0 hydrogen bonds · protein-protein
- T–C · 32 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3B0D · Crystal structure of the chicken CENP-T histone fold/CENP-W complex, crystal form II · the same entry in another collection · chain T against T, TM-score 1.00
- F1NPG5 · AlphaFold monomer V2.0 prediction for centromere protein T (F1NPG5) · a predicted model of the same protein · chain T against A, TM-score 0.99
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 F1NPG5
- Elsewhere: RCSB PDB 3B0D · PDBe 3B0D · UniProt F1NPG5
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