MolNFT v1 · #127527 · protein
The dblb domain of PF11_0521 PFEMP1 bound to human icam-1
5MZA · Erythrocyte membrane protein 1 (PFEMP1): “The dblb domain of PF11_0521 PFEMP1 bound to human icam-1”. X-ray diffraction, 3 ligands (3PO, IHP, NAG), 4 pockets (best druggability 0.72). MolNFT v1 #127527 on GenesisL1: 3D structure…
- PDB
- 5MZA
- Type
- protein
- Length
- 626 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Erythrocyte membrane protein 1 (PFEMP1); Intercellular adhesion molecule 1
- UniProt
- Q8IHM0, P05362
- Ligands
- 3PO, IHP, NAG
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Erythrocyte membrane protein 1 (PFEMP1) | protein | 440 | 53% helix, 2% strand | Q8IHM0 |
| B | Intercellular adhesion molecule 1 | protein | 186 | 5% helix, 61% strand | P05362 |
Ligands and binding sites
- 3PO · Triphosphate · ligand · chains A
- IHP · Inositol hexakisphosphate · ligand · chains B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 499 | 0.72 | 0.81 | 56 | empty |
| 2 | 278 | 0.57 | 0.77 | 30 | empty |
| 3 | 139 | 0.45 | 0.76 | 27 | empty |
| 4 | 94 | 0.43 | 0.79 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1196 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 5MZA · The DBLb domain of PF11_0521 PfEMP1 bound to human ICAM-1 · the same entry in another collection · chain A against A, TM-score 1.00
- P05362 · AlphaFold monomer V2.0 prediction for intercellular adhesion molecule 1 (P05362) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 Q8IHM0
- Every structure of UniProt P05362
- Elsewhere: RCSB PDB 5MZA · PDBe 5MZA · UniProt Q8IHM0 · UniProt P05362
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