MolNFT v1 · #179833 · protein
Cryoem structure of LILRB1 D3D4 domain-inserted antibody MDB1 Fab in complex with plasmodium rifin (PF3D7_1373400) V2 domain
7KHF · MDB1 Fab heavy chain: “Cryoem structure of LILRB1 D3D4 domain-inserted antibody MDB1 Fab in complex with plasmodium rifin…”. Electron microscopy, 1 ligand (NAG), 15 pockets (best druggability 0.76). MolNFT v1 #179833 on GenesisL1…
- PDB
- 7KHF
- Type
- protein
- Length
- 1,516 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MDB1 Fab heavy chain; MDB1 Fab light chain; Rifin
- UniProt
- C0H5N9
- Ligands
- NAG
- Pockets
- 15 · best druggability 0.76
Structure
electron microscopy · 3 distinct chains · 12% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, A | MDB1 Fab heavy chain | protein | 426 | 3% helix, 45% strand | — |
| L, B | MDB1 Fab light chain | protein | 214 | 6% helix, 44% strand | — |
| D, C | Rifin | protein | 118 | 58% helix, 2% strand | C0H5N9 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains H, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1181 | 0.76 | 0.79 | 123 | empty |
| 2 | 695 | 0.71 | 0.78 | 64 | empty |
| 3 | 569 | 0.64 | 0.76 | 58 | empty |
| 4 | 551 | 0.63 | 0.75 | 52 | empty |
| 5 | 246 | 0.56 | 0.78 | 38 | empty |
Interfaces
8 interfaces between chains.
- H–B · 2003 Ų buried · 13 hydrogen bonds · protein-protein
- L–A · 1947 Ų buried · 11 hydrogen bonds · protein-protein
- H–A · 1840 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 1044 Ų buried · 11 hydrogen bonds · protein-protein
- H–C · 992 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 7KHF · CryoEM structure of LILRB1 D3D4 domain-inserted antibody MDB1 Fab in complex with… · the same entry in another collection · chain H against H, 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 C0H5N9
- Elsewhere: RCSB PDB 7KHF · PDBe 7KHF · UniProt C0H5N9
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