MolNFT v1 · #67421 · protein
Structure of S67-27 in complex with KDO(2.8)KDO
3IJY · Immunoglobulin light chain (IGG3): “Structure of S67-27 in complex with KDO(2.8)KDO”. X-ray diffraction, 3 ligands (KDA, KDO, MG), 8 pockets (best druggability 0.72). MolNFT v1 #67421 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3IJY
- Type
- protein
- Length
- 873 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
- KDA, KDO, MG
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Immunoglobulin light chain (IGG3) | protein | 215 | 6% helix, 53% strand | — |
| B | Immunoglobulin heavy chain (IGG3) | protein | 221 | 8% helix, 48% strand | — |
| C | Immunoglobulin light chain (IGG3) | protein | 217 | 6% helix, 53% strand | — |
| D | Immunoglobulin heavy chain (IGG3) | protein | 220 | 5% helix, 50% strand | — |
Ligands and binding sites
- KDA · prop-2-en-1-yl 3-deoxy-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
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1154 | 0.72 | 0.76 | 101 | empty |
| 2 | 477 | 0.70 | 0.81 | 83 | empty |
| 3 | 624 | 0.64 | 0.75 | 60 | empty |
| 4 | 102 | 0.35 | 0.74 | 25 | empty |
| 5 | 83 | 0.34 | 0.75 | 16 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1840 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1822 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 384 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 209 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 162 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3IJY · Structure of S67-27 in Complex with Kdo(2.8)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 3IJY · PDBe 3IJY
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