Research workbench
Structure of protective antibody 38-1-10A Fab
Analyse Structure of protective antibody 38-1-10A Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Z3K
- Type
- protein
- Length
- 3,850 residues
- Chains
- 18
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heavy chain; Light chain
- Pockets
- 20 · best druggability 0.67
Structure
x-ray diffraction · 6 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, C, E, G | Heavy chain | protein | 216 | 8% helix, 52% strand | — |
| L, K, N, P, R | Light chain | protein | 213 | 7% helix, 52% strand | — |
| A | Heavy chain | protein | 214 | 6% helix, 54% strand | — |
| B | Light chain | protein | 211 | 7% helix, 52% strand | — |
| D, F, I | Light chain | protein | 212 | 5% helix, 51% strand | — |
| J, M, O, Q | Heavy chain | protein | 215 | 6% helix, 53% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 5 copies · chains H, L, I, G, M, N, J, K, O, P, Q, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 640 | 0.67 | 0.76 | 78 | empty |
| 2 | 536 | 0.64 | 0.76 | 70 | empty |
| 3 | 689 | 0.64 | 0.74 | 61 | empty |
| 4 | 650 | 0.63 | 0.74 | 59 | empty |
| 5 | 653 | 0.63 | 0.74 | 65 | empty |
Interfaces
29 interfaces between chains.
- E–F · 1950 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1944 Ų buried · 20 hydrogen bonds · protein-protein
- H–L · 1942 Ų buried · 23 hydrogen bonds · protein-protein
- O–P · 1938 Ų buried · 23 hydrogen bonds · protein-protein
- M–N · 1927 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide (disulfide).
Compared structures
- 6Z3K · Structure of protective antibody 38-1-10A Fab · 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 6Z3K · PDBe 6Z3K
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