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High resolution crystal structure of the complex of the hydrolytic antibody Fab 6D9 and a transition-state analog
Analyse High resolution crystal structure of the complex of the hydrolytic antibody Fab… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DQT
- Type
- protein
- Length
- 437 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin 6D9
- Ligands
- CPD
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Immunoglobulin 6D9 | protein | 219 | 5% helix, 51% strand | — |
| H | Immunoglobulin 6D9 | protein | 218 | 6% helix, 52% strand | — |
Ligands and binding sites
- CPD · [1-(3-dimethylamino-propyl)-3-ethyl-ureido]-[4-(2,2,2-trifluoro-acetylamino)-benzyl]phosphinic acid-2-(2,2-dihydro-acetylamino)-3-hydroxy-1-(4-nitrophenyl)-propyl ester · ligand · chains L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 169 | 0.63 | 0.84 | 23 | CPD |
| 2 | 375 | 0.56 | 0.74 | 52 | empty |
| 3 | 77 | 0.34 | 0.76 | 16 | empty |
| 4 | 64 | 0.30 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- L–H · 2030 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 2DQT · High resolution crystal structure of the complex of the hydrolytic antibody Fab 6D9 and a… · the same entry in another collection · chain L against L, 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 2DQT · PDBe 2DQT
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