MolNFT v1 · #134287 · protein
Structure of human N-terminally engineered RAB1B in complex with the bmerb domain of mical-cl
5SZK · Mical C-terminal-like protein: “Structure of human N-terminally engineered RAB1B in complex with the bmerb domain of mical-cl”. X-ray diffraction, 2 ligands (GNP, MG), 1 pocket (best druggability 0.77). MolNFT v1 #134287 on…
- PDB
- 5SZK
- Type
- protein
- Length
- 313 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mical C-terminal-like protein; RAS-related protein rab-1B
- UniProt
- Q6ZW33, Q9H0U4
- Ligands
- GNP, MG
- Pockets
- 1 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 57% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mical C-terminal-like protein | protein | 140 | 85% helix, 0% strand | Q6ZW33 |
| B | RAS-related protein rab-1B | protein | 173 | 34% helix, 27% strand | Q9H0U4 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains B
- MG · Magnesium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 931 | 0.77 | 0.79 | 84 | MG, GNP |
Interfaces
1 interface between chains.
- A–B · 923 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5SZK · Structure of human N-terminally engineered Rab1b in complex with the bMERB domain of… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9H0U4 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-1B (Q9H0U4) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q6ZW33
- Every structure of UniProt Q9H0U4
- Elsewhere: RCSB PDB 5SZK · PDBe 5SZK · UniProt Q6ZW33 · UniProt Q9H0U4
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