Research workbench
Single-chain fv antibody of C6 complexed with 2-(4-hydroxy-3- NITROPHENYL)ACETIC acid
Analyse Single-chain fv antibody of C6 complexed with 2-(4-hydroxy-3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6K4Z
- Type
- protein
- Length
- 454 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Scfv of C6
- Ligands
- NPA, SO4
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Scfv of C6 | protein | 227 | 8% helix, 52% strand | — |
| B | Scfv of C6 | protein | 227 | 7% helix, 53% strand | — |
Ligands and binding sites
- NPA · 2-(4-hydroxy-3-nitrophenyl)acetic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 482 | 0.62 | 0.75 | 48 | empty |
| 2 | 91 | 0.34 | 0.74 | 25 | empty |
| 3 | 80 | 0.32 | 0.74 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 314 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6K4Z · Single-chain Fv antibody of C6 COMPLEXED WITH 2-(4-HYDROXY-3-NITROPHENYL)ACETIC ACID · 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 6K4Z · PDBe 6K4Z
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