MolNFT v2 · #197118 · protein
Pfs230 domain 1 bound by RUPA-32 Fab
7UVH · RUPA-32 Fab Heavy Chain: “Pfs230 domain 1 bound by RUPA-32 Fab”. X-ray diffraction at 2.59, 2 ligands (CL, NH4), 13 pockets (best druggability 0.67). MolNFT v2 #197118 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7UVH
- Type
- protein
- Length
- 1,206 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.59
- Source
- Homo sapiens; Plasmodium falciparum
- Molecule
- RUPA-32 Fab Heavy Chain; RUPA-32 Fab Light Chain; Gametocyte surface protein P230
- UniProt
- P68874
- Ligands
- CL, NH4
- Pockets
- 13 · best druggability 0.67
Structure
x-ray diffraction · resolution 2.59 · 5 distinct chains · 6% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | RUPA-32 Fab Heavy Chain | protein | 222 | 7% helix, 50% strand | — |
| B | RUPA-32 Fab Light Chain | protein | 215 | 6% helix, 51% strand | — |
| C | Gametocyte surface protein P230 | protein | 165 | 4% helix, 44% strand | P68874 |
| E | RUPA-32 Fab Light Chain | protein | 211 | 9% helix, 52% strand | — |
| F | Gametocyte surface protein P230 | protein | 171 | 4% helix, 43% strand | P68874 |
Ligands and binding sites
- CL · Chloride ion · ion · 10 copies · chains A, B, D
- NH4 · Ammonium ion · ion · 2 copies · chains A, D
- EDO · 1,2-ethanediol · additive · 3 copies · chains B, A, C, E
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 703 | 0.67 | 0.76 | 77 | empty |
| 2 | 370 | 0.55 | 0.74 | 40 | EDO |
| 3 | 255 | 0.55 | 0.77 | 36 | NH4 |
| 4 | 214 | 0.49 | 0.75 | 36 | CL |
| 5 | 259 | 0.48 | 0.73 | 45 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1938 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 1829 Ų buried · 14 hydrogen bonds · protein-protein
- A–E · 678 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 534 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 480 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
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 P68874
- Elsewhere: RCSB PDB 7UVH · PDBe 7UVH · UniProt P68874
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