Research workbench
Crystal structure of the IGG2A LPT3 in complex with an 8-sugar inner core analogue of neisseria meningitidis
Analyse Crystal structure of the IGG2A LPT3 in complex with an 8-sugar inner core… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4C83
- Type
- protein
- Length
- 857 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LPT3 heavy chain; LPT3 light chain
- Ligands
- GMH, KDO, NDG, BGC, SO4
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | LPT3 heavy chain | protein | 215 | 4% helix, 55% strand | — |
| B | LPT3 light chain | protein | 214 | 5% helix, 49% strand | — |
| D | LPT3 light chain | protein | 213 | 6% helix, 50% strand | — |
Ligands and binding sites
- GMH · L-glycero-alpha-D-manno-heptopyranose · sugar · 4 copies · chains A, C
- KDO · 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid · sugar · 2 copies · chains A, C
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 2 copies · chains A, B, C, D
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains A, C
- SO4 · Sulfate ion · ion · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 914 | 0.73 | 0.77 | 81 | empty |
| 2 | 334 | 0.64 | 0.79 | 40 | empty |
| 3 | 461 | 0.58 | 0.74 | 48 | empty |
| 4 | 173 | 0.51 | 0.78 | 23 | empty |
| 5 | 92 | 0.37 | 0.76 | 20 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1948 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1937 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 472 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 268 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 13 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 4C83 · Crystal Structure of the IgG2a LPT3 in complex with an 8-sugar inner core analogue of… · 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 4C83 · PDBe 4C83
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