Research workbench
Crystal structure of S25-39 in complex with kdo
Analyse Crystal structure of S25-39 in complex with kdo in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OKD
- Type
- protein
- Length
- 437 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S25-39 Fab (IGG1K) light chain; S25-39 Fab (IGG1K) heavy chain
- Ligands
- KDO, ZN
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S25-39 Fab (IGG1K) light chain | protein | 219 | 7% helix, 53% strand | — |
| B | S25-39 Fab (IGG1K) heavy chain | protein | 218 | 7% helix, 49% strand | — |
Ligands and binding sites
- KDO · 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid · sugar · chains A, B
- ZN · Zinc ion · metal · chains B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 614 | 0.63 | 0.74 | 60 | PEG |
| 2 | 73 | 0.52 | 0.86 | 23 | empty |
| 3 | 181 | 0.45 | 0.75 | 31 | empty |
| 4 | 72 | 0.31 | 0.74 | 19 | empty |
| 5 | 56 | 0.24 | 0.72 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1769 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3OKD · Crystal structure of S25-39 in complex with Kdo · 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 3OKD · PDBe 3OKD
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