MolNFT v1 · #49880 · protein
Crystal structure of S25-2 Fab in complex with kdo analogues
2R1X · Fab, antibody fragment (IGG1K), light chain: “Crystal structure of S25-2 Fab in complex with kdo analogues”. X-ray diffraction, 4 ligands (KDA, KDD, MG), 2 pockets (best druggability 0.62). MolNFT v1 #49880 on GenesisL1: 3D…
- PDB
- 2R1X
- Type
- protein
- Length
- 434 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab, antibody fragment (IGG1K), light chain; Fab, antibody fragment (IGG1K), heavy chain
- Ligands
- KDA, KDD, MG, ZN
- Pockets
- 2 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fab, antibody fragment (IGG1K), light chain | protein | 219 | 6% helix, 53% strand | — |
| B | Fab, antibody fragment (IGG1K), heavy chain | protein | 215 | 8% helix, 50% strand | — |
Ligands and binding sites
- KDA · prop-2-en-1-yl 3-deoxy-alpha-D-manno-oct-2-ulopyranosidonic acid · ligand · chains A, B
- KDD · 2,6-anhydro-3,5-dideoxy-D-ribo-oct-2-enonic acid · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A, B
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 557 | 0.62 | 0.75 | 56 | empty |
| 2 | 77 | 0.30 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1839 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2R1X · Crystal structure of S25-2 Fab in complex with Kdo analogues · 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 2R1X · PDBe 2R1X
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