MolNFT v1 · #146893 · protein
Structure of the 6078 antibody Fab fragment bound to a staphylococcus aureus wall techoic acid analog
6DW2 · 6078 Fab light chain: “Structure of the 6078 antibody Fab fragment bound to a staphylococcus aureus wall techoic acid analog”. X-ray diffraction, 2 ligands (HD4, NA), 6 pockets (best druggability 0.67). MolNFT v1 #146893 on…
- PDB
- 6DW2
- Type
- protein
- Length
- 440 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6078 Fab light chain; 6078 Fab heavy chain
- Ligands
- HD4, NA
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 6078 Fab light chain | protein | 213 | 6% helix, 51% strand | — |
| B | 6078 Fab heavy chain | protein | 227 | 9% helix, 49% strand | — |
Ligands and binding sites
- HD4 · 4-O-[2-acetamido-2-deoxy-beta-D-glucopyranosyl]-1-O-phosphono-D-ribitol · ligand · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- MLA · Malonic acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 757 | 0.67 | 0.75 | 76 | empty |
| 2 | 50 | 0.51 | 0.88 | 18 | empty |
| 3 | 158 | 0.45 | 0.75 | 27 | empty |
| 4 | 61 | 0.39 | 0.80 | 16 | empty |
| 5 | 72 | 0.37 | 0.78 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 2080 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6DW2 · Structure of the 6078 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 6DW2 · PDBe 6DW2
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