Research workbench
Structure of 4497 Fab bound to synthetic wall teichoic acid fragment
Analyse Structure of 4497 Fab bound to synthetic wall teichoic acid fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5D6C
- Type
- protein
- Length
- 867 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4497 antibody igk (vl and cl); 4497 antibody IGG1 (vh and CH1)
- Ligands
- 57S, CA
- Pockets
- 10 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, L | 4497 antibody igk (vl and cl) | protein | 219 | 7% helix, 52% strand | — |
| B | 4497 antibody IGG1 (vh and CH1) | protein | 210 | 9% helix, 53% strand | — |
| H | 4497 antibody IGG1 (vh and CH1) | protein | 219 | 7% helix, 50% strand | — |
Ligands and binding sites
- 57S · 4-O-[2-acetamido-2-deoxy-beta-D-glucopyranosyl]-5-O-phosphono-D-ribitol · ligand · 2 copies · chains A, B, H, L
- CA · Calcium ion · metal · 4 copies · chains A, B, L, H
- ACT · Acetate ion · additive · 2 copies · chains H, L
- GOL · Glycerol · additive · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1069 | 0.70 | 0.75 | 98 | ACT |
| 2 | 640 | 0.66 | 0.75 | 62 | CA |
| 3 | 302 | 0.58 | 0.77 | 37 | GOL |
| 4 | 53 | 0.56 | 0.90 | 19 | empty |
| 5 | 56 | 0.49 | 0.87 | 22 | empty |
Interfaces
4 interfaces between chains.
- H–L · 1789 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1728 Ų buried · 14 hydrogen bonds · protein-protein
- A–L · 685 Ų buried · 10 hydrogen bonds · protein-protein
- A–H · 29 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5D6C · Structure of 4497 Fab bound to synthetic wall teichoic acid fragment · 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 5D6C · PDBe 5D6C
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