MolNFT v1 · #134284 · protein
Structure of human RAB1B in complex with the bmerb domain of mical-cl
5SZH · Mical C-terminal-like protein: “Structure of human RAB1B in complex with the bmerb domain of mical-cl”. X-ray diffraction, 2 ligands (GNP, MG), 2 pockets (best druggability 0.79). MolNFT v1 #134284 on GenesisL1: 3D structure…
- PDB
- 5SZH
- Type
- protein
- Length
- 318 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
- 2 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 61% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mical C-terminal-like protein | protein | 143 | 92% helix, 0% strand | Q6ZW33 |
| B | RAS-related protein rab-1B | protein | 175 | 35% helix, 26% 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
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 835 | 0.79 | 0.82 | 76 | GNP, MG |
| 2 | 53 | 0.28 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1205 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5SZH · Structure of human Rab1b in complex with the bMERB domain of Mical-cL · 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 5SZH · PDBe 5SZH · UniProt Q6ZW33 · UniProt Q9H0U4
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