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Crystal structure of S54-10 antibody in complex with antigen KDO(2.4) KDO(2.4)KDO
Analyse Crystal structure of S54-10 antibody in complex with antigen KDO(2.4)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3I02
- Type
- protein
- Length
- 847 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin light chain; Immunoglobulin heavy chain
- Ligands
- KDA, KDO
- Pockets
- 16 · best druggability 0.62
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Immunoglobulin light chain | protein | 219 | 7% helix, 53% strand | — |
| B | Immunoglobulin heavy chain | protein | 220 | 8% helix, 47% strand | — |
| C | Immunoglobulin light chain | protein | 196 | 5% helix, 51% strand | — |
| D | Immunoglobulin heavy chain | protein | 212 | 6% helix, 47% 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 · 4 copies · chains B, A, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 311 | 0.62 | 0.79 | 53 | empty |
| 2 | 172 | 0.53 | 0.80 | 32 | empty |
| 3 | 140 | 0.52 | 0.80 | 25 | empty |
| 4 | 86 | 0.44 | 0.80 | 19 | empty |
| 5 | 94 | 0.40 | 0.77 | 20 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1903 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1897 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 503 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 10 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3I02 · Crystal structure of S54-10 antibody in complex with antigen Kdo(2.4)Kdo(2.4)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 3I02 · PDBe 3I02
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