Research workbench
Structure of the N-terminal nts-DBL1-alpha and cidr-gamma double domain of the PFEMP1 protein from plasmodium falciparum varo strain.
Analyse Structure of the N-terminal nts-DBL1-alpha and cidr-gamma double domain of the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YK0
- Type
- protein
- Length
- 698 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Erythrocyte membrane protein 1
- UniProt
- B7T1P0
- Ligands
- MG, SO4
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Erythrocyte membrane protein 1 | protein | 698 | 48% helix, 8% strand | B7T1P0 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 811 | 0.80 | 0.83 | 63 | SO4 |
| 2 | 53 | 0.67 | 0.96 | 20 | empty |
| 3 | 285 | 0.59 | 0.78 | 28 | empty |
| 4 | 160 | 0.58 | 0.82 | 31 | empty |
| 5 | 110 | 0.57 | 0.85 | 23 | empty |
Modifications
Observed in the structure: 15 disulfide (disulfide).
Compared structures
- 2YK0 · Structure of the N-terminal NTS-DBL1-alpha and CIDR-gamma double domain of the PfEMP1… · 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 B7T1P0
- Elsewhere: RCSB PDB 2YK0 · PDBe 2YK0 · UniProt B7T1P0
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