MolNFT v1 · #32308 · protein
High resolution structure of gppnhp-bound human RAB4A
2BME · RAS-related protein RAB4A: “High resolution structure of gppnhp-bound human RAB4A”. X-ray diffraction, 2 ligands (GNP, MG), 10 pockets (best druggability 0.73). MolNFT v1 #32308 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 2BME
- Type
- protein
- Length
- 697 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein RAB4A
- EC
- 3.6.5.2
- UniProt
- P20338
- Ligands
- GNP, MG
- Pockets
- 10 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAS-related protein RAB4A (EC 3.6.5.2) | protein | 176 | 38% helix, 27% strand | P20338 |
| B | RAS-related protein RAB4A (EC 3.6.5.2) | protein | 173 | 39% helix, 28% strand | P20338 |
| C, D | RAS-related protein RAB4A (EC 3.6.5.2) | protein | 174 | 39% helix, 27% strand | P20338 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 4 copies · chains A, C, B, D
- BME · Beta-mercaptoethanol · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1037 | 0.73 | 0.76 | 92 | empty |
| 2 | 149 | 0.60 | 0.84 | 27 | TRS |
| 3 | 325 | 0.56 | 0.76 | 40 | empty |
| 4 | 125 | 0.49 | 0.80 | 26 | GNP, MG |
| 5 | 131 | 0.49 | 0.79 | 26 | GNP, MG |
Interfaces
4 interfaces between chains.
- A–C · 867 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 409 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 284 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 79 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
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
- Elsewhere: RCSB PDB 2BME · PDBe 2BME · UniProt P20338
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