MolNFT v1 · #187095 · protein
Structures of tcdb in complex with R-RAS
7S0Z · Toxin B: “Structures of tcdb in complex with R-RAS”. X-ray diffraction, 6 ligands (UDP, GDP, GLC), 15 pockets (best druggability 0.83). MolNFT v1 #187095 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7S0Z
- Type
- protein
- Length
- 1,440 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toxin B; RAS-related protein R-RAS
- EC
- 2.4.1.-, 3.6.5.-
- UniProt
- M4NKV9, P10301
- Ligands
- UDP, GDP, GLC, MG, MN, NH4
- Pockets
- 15 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Toxin B (EC 2.4.1.-) | protein | 541 | 58% helix, 8% strand | M4NKV9 |
| C, D | RAS-related protein R-RAS (EC 3.6.5.-) | protein | 179 | 38% helix, 23% strand | P10301 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains B, D, A, C
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, C, B, D
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains B, D, A, C
- MG · Magnesium ion · metal · 5 copies · chains A, C, B, D
- MN · Manganese (II) ion · metal · 2 copies · chains B, A
- NH4 · Ammonium ion · ion · 9 copies · chains B, A, C
- ACT · Acetate ion · additive · 15 copies · chains B, C, A, D
- EDO · 1,2-ethanediol · additive · 13 copies · chains B, D, C, A
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1093 | 0.83 | 0.84 | 112 | UDP, NH4, MN, MG, GLC, EDO, GDP |
| 2 | 1030 | 0.82 | 0.83 | 104 | UDP, ACT, MN, GLC, GDP, MG |
| 3 | 982 | 0.78 | 0.80 | 83 | EDO, ACT |
| 4 | 657 | 0.77 | 0.83 | 50 | ACT |
| 5 | 235 | 0.60 | 0.80 | 33 | NH4 |
Interfaces
6 interfaces between chains.
- B–D · 2087 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 2068 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 908 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 896 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 215 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 M4NKV9
- Every structure of UniProt P10301
- Elsewhere: RCSB PDB 7S0Z · PDBe 7S0Z · UniProt M4NKV9 · UniProt P10301
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.