MolNFT v1 · #135626 · protein
Rta-V1C7-G29R-NO_SALT
5U4M · Ricin: “Rta-V1C7-G29R-NO_SALT”. X-ray diffraction, 1 ligand (CL), 3 pockets (best druggability 0.53). MolNFT v1 #135626 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5U4M
- Type
- protein
- Length
- 384 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ricin; V1C7 vhh antibody
- EC
- 3.2.2.22
- UniProt
- P02879
- Ligands
- CL
- Pockets
- 3 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ricin (EC 3.2.2.22) | protein | 255 | 41% helix, 23% strand | P02879 |
| B | V1C7 vhh antibody | protein | 129 | 7% helix, 47% strand | — |
Ligands and binding sites
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 237 | 0.53 | 0.76 | 29 | empty |
| 2 | 141 | 0.50 | 0.79 | 21 | empty |
| 3 | 56 | 0.35 | 0.79 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 738 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5U4M · RTA-V1C7-G29R-no_salt · the same entry in another collection · chain A against A, TM-score 1.00
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 P02879
- Elsewhere: RCSB PDB 5U4M · PDBe 5U4M · UniProt P02879
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