Research workbench
Crystal structure of S25-39 in complex with KDO(2.8)KDO(2.4)KDO
Analyse Crystal structure of S25-39 in complex with KDO(2.8)KDO(2.4)KDO in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OKO
- Type
- protein
- Length
- 436 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
- KDA, KDO, ZN
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | S25-39 Fab (IGG1K) light chain | protein | 219 | 5% helix, 49% strand | — |
| A | S25-39 Fab (IGG1K) heavy chain | protein | 217 | 6% helix, 52% strand | — |
Ligands and binding sites
- KDA · prop-2-en-1-yl 3-deoxy-alpha-D-manno-oct-2-ulopyranosidonic acid · ligand · chains A
- KDO · 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid · sugar · 2 copies · chains B, A
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 563 | 0.61 | 0.74 | 61 | empty |
| 2 | 166 | 0.45 | 0.75 | 28 | empty |
| 3 | 64 | 0.45 | 0.83 | 18 | empty |
| 4 | 69 | 0.27 | 0.72 | 15 | empty |
Interfaces
1 interface between chains.
- B–A · 1811 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3OKO · Crystal structure of S25-39 in complex with Kdo(2.8)Kdo(2.4)Kdo · the same entry in another collection · chain B against B, 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 3OKO · PDBe 3OKO
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.