MolNFT v1 · #67556 · protein
Crystal structure of an unbound KZ52 neutralizing anti-ebolavirus antibody.
3INU · KZ52 antibody fragment heavy chain: “Crystal structure of an unbound KZ52 neutralizing anti-ebolavirus antibody.”. X-ray diffraction, 1 ligand (SO4), 7 pockets (best druggability 0.75). MolNFT v1 #67556 on GenesisL1: 3D structure…
- PDB
- 3INU
- Type
- protein
- Length
- 885 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- KZ52 antibody fragment heavy chain; KZ52 antibody fragment light chain
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | KZ52 antibody fragment heavy chain | protein | 226 | 11% helix, 50% strand | — |
| L, N | KZ52 antibody fragment light chain | protein | 217 | 6% helix, 52% strand | — |
| M | KZ52 antibody fragment heavy chain | protein | 225 | 10% helix, 51% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains H, L, M, N
- GOL · Glycerol · additive · 4 copies · chains H, L, M, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1172 | 0.75 | 0.78 | 116 | SO4 |
| 2 | 639 | 0.64 | 0.74 | 59 | empty |
| 3 | 66 | 0.50 | 0.86 | 21 | empty |
| 4 | 99 | 0.48 | 0.81 | 21 | empty |
| 5 | 66 | 0.29 | 0.73 | 17 | empty |
Interfaces
4 interfaces between chains.
- M–N · 1839 Ų buried · 9 hydrogen bonds · protein-protein
- H–L · 1816 Ų buried · 12 hydrogen bonds · protein-protein
- L–M · 523 Ų buried · 6 hydrogen bonds · protein-protein
- L–N · 130 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3INU · Crystal structure of an unbound KZ52 neutralizing anti-Ebolavirus antibody. · 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
- Elsewhere: RCSB PDB 3INU · PDBe 3INU
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