Research workbench
Structure of S67-27 in complex with KDO(2.8)-7-O-methyl-kdo
Analyse Structure of S67-27 in complex with KDO(2.8)-7-O-methyl-kdo in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IKC
- Type
- protein
- Length
- 876 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin light chain (IGG3); Immunoglobulin heavy chain (IGG3)
- Ligands
- KME, KDO, MG
- Pockets
- 10 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Immunoglobulin light chain (IGG3) | protein | 217 | 6% helix, 53% strand | — |
| B, D | Immunoglobulin heavy chain (IGG3) | protein | 221 | 8% helix, 48% strand | — |
Ligands and binding sites
- KME · (1E)-prop-1-en-1-yl 3-deoxy-7-O-methyl-alpha-D-manno-oct-2-ulopyranosidonic acid · ligand · 2 copies · chains A, B, C, D
- KDO · 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid · sugar · 2 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 842 | 0.69 | 0.75 | 70 | empty |
| 2 | 677 | 0.65 | 0.74 | 60 | empty |
| 3 | 297 | 0.64 | 0.81 | 47 | empty |
| 4 | 365 | 0.60 | 0.76 | 37 | empty |
| 5 | 108 | 0.53 | 0.83 | 23 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1853 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1813 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 355 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 197 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 148 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3IKC · Structure of S67-27 in Complex with Kdo(2.8)-7-O-methyl-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 3IKC · PDBe 3IKC
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