Research workbench
Intraflagellar transport complex 25-27 from chlamydomonas
Analyse Intraflagellar transport complex 25-27 from chlamydomonas in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YC2
- Type
- protein
- Length
- 561 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
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Intraflagellar transport protein 25 | protein | 132 | 4% helix, 56% strand | B8LIX8 |
| C | Small rab-related GTPase | protein | 149 | 41% helix, 27% strand | A8HN58 |
| D | Small rab-related GTPase | protein | 148 | 40% helix, 27% strand | A8HN58 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 130 | 0.68 | 0.89 | 24 | empty |
| 2 | 531 | 0.66 | 0.77 | 55 | empty |
| 3 | 72 | 0.57 | 0.88 | 22 | empty |
| 4 | 76 | 0.34 | 0.75 | 22 | empty |
| 5 | 51 | 0.30 | 0.76 | 16 | empty |
Interfaces
5 interfaces between chains.
- B–C · 1129 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 1127 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 295 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 64 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 26 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2YC2 · Intraflagellar Transport Complex 25-27 from Chlamydomonas · the same entry in another collection · chain A against A, 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 2YC2 · PDBe 2YC2 · UniProt B8LIX8 · UniProt A8HN58
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