Research workbench
Structure of the 4497 antibody Fab fragment bound to a staphylococcus aureus wall techoic acid analog
Analyse Structure of the 4497 antibody Fab fragment bound to a staphylococcus aureus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DWA
- Type
- protein
- Length
- 860 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4497 Fab light chain; 4497 Fab heavy chain
- Ligands
- HD4
- Pockets
- 11 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4497 Fab light chain | protein | 217 | 6% helix, 52% strand | — |
| B | 4497 Fab heavy chain | protein | 211 | 9% helix, 53% strand | — |
| H | 4497 Fab heavy chain | protein | 213 | 8% helix, 52% strand | — |
| L | 4497 Fab light chain | protein | 219 | 7% helix, 52% strand | — |
Ligands and binding sites
- HD4 · 4-O-[2-acetamido-2-deoxy-beta-D-glucopyranosyl]-1-O-phosphono-D-ribitol · ligand · 2 copies · chains A, B, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 627 | 0.67 | 0.77 | 54 | empty |
| 2 | 621 | 0.65 | 0.75 | 59 | empty |
| 3 | 509 | 0.60 | 0.74 | 52 | empty |
| 4 | 64 | 0.56 | 0.89 | 19 | empty |
| 5 | 65 | 0.54 | 0.88 | 24 | empty |
Interfaces
4 interfaces between chains.
- H–L · 1813 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1771 Ų buried · 16 hydrogen bonds · protein-protein
- A–L · 706 Ų buried · 15 hydrogen bonds · protein-protein
- A–H · 117 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 6DWA · Structure of the 4497 Antibody Fab fragment bound to a Staphylococcus aureus wall techoic… · 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
- Elsewhere: RCSB PDB 6DWA · PDBe 6DWA
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