MolNFT v1 · #122595 · protein
Crystal structure of the sac domain of cpap in a complex with tubulin and darpin
5ITZ · Tubulin alpha-1B chain: “Crystal structure of the sac domain of cpap in a complex with tubulin and darpin”. X-ray diffraction, 4 ligands (GTP, GDP, LOC), 8 pockets (best druggability 0.84). MolNFT v1 #122595 on GenesisL1: 3D…
- PDB
- 5ITZ
- Type
- protein
- Length
- 990 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1B chain; Tubulin beta-2B chain; Centromere protein J; Designed ankyrin…
- UniProt
- P81947, Q6B856, Q9HC77
- Ligands
- GTP, GDP, LOC, MG
- Pockets
- 8 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1B chain | protein | 430 | 45% helix, 17% strand | P81947 |
| B | Tubulin beta-2B chain | protein | 420 | 49% helix, 18% strand | Q6B856 |
| D | Centromere protein J | protein | 13 | 38% helix, 0% strand | Q9HC77 |
| F | Designed ankyrin repeat protein (darpin) D1 | protein | 127 | 54% helix, 0% strand | — |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains A, B
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- LOC · N-[(7S)-1,2,3,10-tetramethoxy-9-oxo-6,7-dihydro-5H-benzo[d]heptalen-7-yl]ethanamide · ligand · chains A, B
- MG · Magnesium ion · metal · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 986 | 0.84 | 0.85 | 99 | GTP, MG, LOC |
| 2 | 171 | 0.60 | 0.83 | 37 | GDP |
| 3 | 187 | 0.56 | 0.80 | 42 | empty |
| 4 | 127 | 0.52 | 0.81 | 25 | empty |
| 5 | 115 | 0.49 | 0.80 | 22 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1354 Ų buried · 17 hydrogen bonds · protein-protein
- B–F · 676 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 644 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 128 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5ITZ · Crystal structure of the SAC domain of CPAP in a complex with Tubulin and Darpin · the same entry in another collection · chain A against A, TM-score 1.00
- Q9HC77 · AlphaFold monomer V2.0 prediction for centromere protein J (Q9HC77) · a predicted model of the same protein · chain D against A, TM-score 0.30
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 P81947
- Every structure of UniProt Q6B856
- Every structure of UniProt Q9HC77
- Elsewhere: RCSB PDB 5ITZ · PDBe 5ITZ · UniProt P81947 · UniProt Q6B856 · UniProt Q9HC77
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