Research workbench
Cryo-EM structure of a plasmodium vivax invasion complex essential for entry into human reticulocytes; two molecules of parasite ligand, subclass 2.
Analyse Cryo-EM structure of a plasmodium vivax invasion complex essential for entry… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6D05
- Type
- protein
- Length
- 3,572 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transferrin receptor protein 1; Serotransferrin; Reticulocyte binding protein 2, putative
- UniProt
- P02786, P02787, A5K736
- Ligands
- NAG, FE, CA, CO3
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 46% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Transferrin receptor protein 1 | protein | 641 | 36% helix, 18% strand | P02786 |
| C, D | Serotransferrin | protein | 679 | 32% helix, 15% strand | P02787 |
| E, F | Reticulocyte binding protein 2, putative | protein | 466 | 82% helix, 1% strand | A5K736 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, B, C, D
- FE · Fe (III) ion · metal · 4 copies · chains C, D
- CA · Calcium ion · metal · 2 copies · chains A, B
- CO3 · Carbonate ion · ion · 4 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 401 | 0.87 | 0.95 | 71 | empty |
| 2 | 760 | 0.80 | 0.84 | 67 | empty |
| 3 | 225 | 0.79 | 0.93 | 39 | empty |
| 4 | 698 | 0.79 | 0.83 | 53 | empty |
| 5 | 250 | 0.77 | 0.90 | 36 | empty |
Interfaces
11 interfaces between chains.
- A–B · 3230 Ų buried · 14 hydrogen bonds · protein-protein
- A–E · 1598 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 1545 Ų buried · 15 hydrogen bonds · protein-protein
- B–F · 1425 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 1370 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 46 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 6D05 · Cryo-EM structure of a Plasmodium vivax invasion complex essential for entry into human… · the same entry in another collection · chain F against F, TM-score 1.00
- P02787 · AlphaFold monomer V2.0 prediction for serotransferrin (P02787) · a predicted model of the same protein · chain C against A, TM-score 0.98
- P02786 · AlphaFold monomer V2.0 prediction for transferrin receptor protein 1 (P02786) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P02786
- Every structure of UniProt P02787
- Every structure of UniProt A5K736
- Elsewhere: RCSB PDB 6D05 · PDBe 6D05 · UniProt P02786 · UniProt P02787 · UniProt A5K736
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