MolNFT v1 · #72858 · protein
Crystal structure of RAB1B covalently modified with AMP at Y77
3NKV · RAS-related protein rab-1B: “Crystal structure of RAB1B covalently modified with AMP at Y77”. X-ray diffraction, 4 ligands (GNP, AMP, MG), 5 pockets (best druggability 0.66). MolNFT v1 #72858 on GenesisL1: 3D structure, binding…
- PDB
- 3NKV
- Type
- protein
- Length
- 339 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein rab-1B
- UniProt
- Q9H0U4
- Ligands
- GNP, AMP, MG, BA
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAS-related protein rab-1B | protein | 170 | 35% helix, 27% strand | Q9H0U4 |
| B | RAS-related protein rab-1B | protein | 169 | 35% helix, 28% strand | Q9H0U4 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains A, B
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- BA · Barium 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 | 510 | 0.66 | 0.77 | 48 | empty |
| 2 | 212 | 0.62 | 0.82 | 33 | GNP, MG |
| 3 | 182 | 0.55 | 0.80 | 29 | GNP, MG |
| 4 | 50 | 0.38 | 0.81 | 15 | empty |
| 5 | 72 | 0.34 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 364 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3NKV · Crystal structure of Rab1b covalently modified with AMP at Y77 · 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 A 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 Q9H0U4
- Elsewhere: RCSB PDB 3NKV · PDBe 3NKV · UniProt Q9H0U4
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