Research workbench
Crystal structure of the chicken SPC24-SPC25 globular domain in complex with cenp-T peptide
Analyse Crystal structure of the chicken SPC24-SPC25 globular domain in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VZA
- Type
- protein
- Length
- 383 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein; SPC24 protein; Centromere protein T
- UniProt
- E1C4Y2, F1NPG5
- Pockets
- 8 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Uncharacterized protein | protein | 99 | 41% helix, 28% strand | E1C4Y2 |
| D, C | SPC24 protein | protein | 62 | 39% helix, 24% strand | — |
| A | Uncharacterized protein | protein | 98 | 42% helix, 29% strand | E1C4Y2 |
| E, F | Centromere protein T | protein | 31 | 52% helix, 0% strand | F1NPG5 |
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 216 | 0.66 | 0.84 | 33 | empty |
| 2 | 211 | 0.52 | 0.77 | 36 | empty |
| 3 | 71 | 0.44 | 0.81 | 20 | empty |
| 4 | 80 | 0.38 | 0.77 | 13 | empty |
| 5 | 87 | 0.35 | 0.75 | 23 | empty |
Interfaces
11 interfaces between chains.
- A–C · 1639 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 1632 Ų buried · 19 hydrogen bonds · protein-protein
- B–F · 922 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 921 Ų buried · 12 hydrogen bonds · protein-protein
- C–E · 573 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3VZA · Crystal structure of the chicken Spc24-Spc25 globular domain in complex with CENP-T… · the same entry in another collection · chain F against F, TM-score 1.00
- F1NPG5 · AlphaFold monomer V2.0 prediction for centromere protein T (F1NPG5) · a predicted model of the same protein · chain E against A, TM-score 0.41
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 E1C4Y2
- Every structure of UniProt F1NPG5
- Elsewhere: RCSB PDB 3VZA · PDBe 3VZA · UniProt E1C4Y2 · UniProt F1NPG5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.