Research workbench
Crystal structure of C-terminally truncated ARL13B from chlamydomonas rheinhardtii bound to gppnhp
Analyse Crystal structure of C-terminally truncated ARL13B from chlamydomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4M9Q
- Type
- protein
- Length
- 582 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arf-like GTPase
- EC
- 3.6.5.2
- UniProt
- A8INQ0
- Ligands
- GNP, MG, SO4
- Pockets
- 11 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Arf-like GTPase (EC 3.6.5.2) | protein | 195 | 44% helix, 22% strand | A8INQ0 |
| B | Arf-like GTPase (EC 3.6.5.2) | protein | 196 | 43% helix, 21% strand | A8INQ0 |
| C | Arf-like GTPase (EC 3.6.5.2) | protein | 191 | 42% helix, 23% strand | A8INQ0 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 164 | 0.54 | 0.80 | 22 | empty |
| 2 | 145 | 0.52 | 0.80 | 32 | SO4 |
| 3 | 119 | 0.50 | 0.81 | 20 | empty |
| 4 | 115 | 0.50 | 0.81 | 25 | empty |
| 5 | 169 | 0.49 | 0.77 | 31 | GNP, MG |
Interfaces
2 interfaces between chains.
- A–B · 886 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 788 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 4M9Q · Crystal structure of C-terminally truncated Arl13B from Chlamydomonas rheinhardtii bound… · the same entry in another collection · chain A against A, TM-score 1.00
- A8INQ0 · AlphaFold monomer V2.0 prediction for ADP-ribosylation factor-like protein 13B (A8INQ0) · a predicted model of the same protein · chain B 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 A8INQ0
- Elsewhere: RCSB PDB 4M9Q · PDBe 4M9Q · UniProt A8INQ0
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