MolNFT v1 · #178614 · protein
Cryo-EM structure of P. falciparum VAR2CSA NF54 core in complex with csa at 3.36 a
7JGH · Erythrocyte membrane protein 1: “Cryo-EM structure of P. falciparum VAR2CSA NF54 core in complex with csa at 3.36 a”. Electron microscopy, 2 ligands (ASG, BDP), 20 pockets (best druggability 0.77). MolNFT v1 #178614 on GenesisL1: 3D…
- PDB
- 7JGH
- Type
- protein
- Length
- 1,421 residues
- Chains
- 1
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Erythrocyte membrane protein 1
- UniProt
- W7K270
- Ligands
- ASG, BDP
- Pockets
- 20 · best druggability 0.77
Structure
electron microscopy · 1 distinct chain · 54% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Erythrocyte membrane protein 1 | protein | 1421 | 54% helix, 1% strand | W7K270 |
Ligands and binding sites
- ASG · 2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose · ligand · 6 copies · chains A
- BDP · beta-D-glucopyranuronic acid · sugar · 6 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 271 | 0.77 | 0.89 | 36 | empty |
| 2 | 326 | 0.77 | 0.88 | 49 | empty |
| 3 | 234 | 0.76 | 0.90 | 39 | BDP, ASG |
| 4 | 299 | 0.75 | 0.87 | 32 | empty |
| 5 | 77 | 0.72 | 0.96 | 18 | empty |
Modifications
Observed in the structure: 26 disulfide (disulfide).
Compared structures
- 7JGH · Cryo-EM structure of P. falciparum VAR2CSA NF54 core in complex with CSA at 3.36 A · 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 W7K270
- Elsewhere: RCSB PDB 7JGH · PDBe 7JGH · UniProt W7K270
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