Research workbench
Structure of GTP-bound RAB4Q67L GTPase in complex with the central rab binding domain of rabenosyn-5
Analyse Structure of GTP-bound RAB4Q67L GTPase in complex with the central rab binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Z0K
- Type
- protein
- Length
- 459 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTP-binding protein; Fyve-finger-containing RAB5 effector protein rabenosyn-5
- UniProt
- P20338, Q59EY8
- Ligands
- GTP, MG
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTP-binding protein | protein | 169 | 36% helix, 28% strand | P20338 |
| B, D | Fyve-finger-containing RAB5 effector protein rabenosyn-5 | protein | 61 | 64% helix, 2% strand | Q59EY8 |
| C | GTP-binding protein | protein | 168 | 38% helix, 29% strand | P20338 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · 2 copies · chains A, C
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 345 | 0.70 | 0.83 | 50 | empty |
| 2 | 98 | 0.49 | 0.81 | 25 | MG, GTP |
| 3 | 87 | 0.45 | 0.80 | 21 | empty |
| 4 | 95 | 0.44 | 0.79 | 25 | MG, GTP |
| 5 | 131 | 0.41 | 0.75 | 23 | empty |
Interfaces
4 interfaces between chains.
- C–D · 978 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 965 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 787 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 202 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1Z0K · Structure of GTP-Bound Rab4Q67L GTPase in complex with the central Rab binding domain of… · the same entry in another collection · chain A against A, TM-score 1.00
- P20338 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-4A (P20338) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P20338
- Every structure of UniProt Q59EY8
- Elsewhere: RCSB PDB 1Z0K · PDBe 1Z0K · UniProt P20338 · UniProt Q59EY8
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