MolNFT v1 · #55173 · protein
Intraflagellar transport complex 25-27 from chlamydomonas
2YC4 · Intraflagellar transport protein 25: “Intraflagellar transport complex 25-27 from chlamydomonas”. X-ray diffraction, 3 ligands (CA, MG, CL), 4 pockets (best druggability 0.66). MolNFT v1 #55173 on GenesisL1: 3D structure, binding…
- PDB
- 2YC4
- Type
- protein
- Length
- 614 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Intraflagellar transport protein 25; Small rab-related GTPase
- UniProt
- B8LIX8, A8HN58
- Ligands
- CA, MG, CL
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 26% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Intraflagellar transport protein 25 | protein | 131 | 5% helix, 57% strand | B8LIX8 |
| B | Intraflagellar transport protein 25 | protein | 131 | 5% helix, 56% strand | B8LIX8 |
| C | Small rab-related GTPase | protein | 177 | 41% helix, 24% strand | A8HN58 |
| D | Small rab-related GTPase | protein | 175 | 41% helix, 23% strand | A8HN58 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains C
- CL · Chloride ion · ion · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.66 | 0.89 | 24 | empty |
| 2 | 111 | 0.64 | 0.88 | 23 | empty |
| 3 | 58 | 0.61 | 0.91 | 18 | empty |
| 4 | 56 | 0.47 | 0.84 | 20 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1147 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1100 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1097 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2YC4 · Intraflagellar Transport Complex 25-27 from Chlamydomonas · the same entry in another collection · chain D against D, TM-score 1.00
- B8LIX8 · AlphaFold monomer V2.0 prediction for intraflagellar transport protein 25 (B8LIX8) · a predicted model of the same protein · chain A against A, TM-score 0.99
- A8HN58 · AlphaFold monomer V2.0 prediction for intraflagellar transport protein 27 (A8HN58) · a predicted model of the same protein · chain D against A, TM-score 0.88
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 B8LIX8
- Every structure of UniProt A8HN58
- Elsewhere: RCSB PDB 2YC4 · PDBe 2YC4 · UniProt B8LIX8 · UniProt A8HN58
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