Research workbench
Structure of the 4462 antibody Fab fragment bound to a staphylococcus aureus wall techoic acid analog
Analyse Structure of the 4462 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
- 6DWI
- Type
- protein
- Length
- 3,337 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4462 Fab light chain; 4462 Fab heavy chain
- Ligands
- HD4, CL
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 11 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G, I, K, O | 4462 Fab light chain | protein | 211 | 5% helix, 52% strand | — |
| B | 4462 Fab heavy chain | protein | 202 | 4% helix, 52% strand | — |
| C | 4462 Fab light chain | protein | 206 | 3% helix, 50% strand | — |
| D, H | 4462 Fab heavy chain | protein | 212 | 7% helix, 52% strand | — |
| E | 4462 Fab light chain | protein | 205 | 6% helix, 53% strand | — |
| F | 4462 Fab heavy chain | protein | 200 | 5% helix, 53% strand | — |
| J | 4462 Fab heavy chain | protein | 214 | 8% helix, 51% strand | — |
| L | 4462 Fab heavy chain | protein | 211 | 7% helix, 52% strand | — |
| M | 4462 Fab light chain | protein | 207 | 6% helix, 52% strand | — |
| N | 4462 Fab heavy chain | protein | 209 | 9% helix, 50% strand | — |
| P | 4462 Fab heavy chain | protein | 204 | 6% helix, 51% strand | — |
Ligands and binding sites
- HD4 · 4-O-[2-acetamido-2-deoxy-beta-D-glucopyranosyl]-1-O-phosphono-D-ribitol · ligand · 4 copies · chains C, D, G, H, I, J, K, L
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D, F, G, H, O, P
- GOL · Glycerol · additive · 2 copies · chains H, J, I
- FLC · Citrate anion · additive · chains G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 850 | 0.82 | 0.85 | 119 | empty |
| 2 | 970 | 0.81 | 0.83 | 153 | empty |
| 3 | 491 | 0.75 | 0.83 | 64 | empty |
| 4 | 782 | 0.72 | 0.78 | 75 | empty |
| 5 | 825 | 0.70 | 0.76 | 83 | GOL |
Interfaces
36 interfaces between chains.
- I–J · 1714 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1695 Ų buried · 10 hydrogen bonds · protein-protein
- K–L · 1687 Ų buried · 9 hydrogen bonds · protein-protein
- G–H · 1670 Ų buried · 14 hydrogen bonds · protein-protein
- M–N · 1666 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 disulfide (disulfide).
Compared structures
- 6DWI · Structure of the 4462 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 6DWI · PDBe 6DWI
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