MolNFT v1 · #184368 · protein
Crystal structure of an antibody targeting the capsular polysaccharide of serogroup X neisseria meningitidis (menx)
7OO2 · Anti-menx Fab heavy chain: “Crystal structure of an antibody targeting the capsular polysaccharide of serogroup X neisseria meningitidis…”. X-ray diffraction, 1 ligand (SCN), 11 pockets (best druggability 0.76). MolNFT v1 #184368 on…
- PDB
- 7OO2
- Type
- protein
- Length
- 864 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-menx Fab heavy chain; Anti-menx Fab light chain
- Ligands
- SCN
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Anti-menx Fab heavy chain | protein | 218 | 6% helix, 51% strand | — |
| B, D | Anti-menx Fab light chain | protein | 214 | 7% helix, 51% strand | — |
Ligands and binding sites
- SCN · Thiocyanate ion · ion · 3 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1049 | 0.76 | 0.79 | 109 | SCN |
| 2 | 881 | 0.75 | 0.79 | 73 | SCN |
| 3 | 240 | 0.66 | 0.84 | 30 | empty |
| 4 | 173 | 0.57 | 0.81 | 28 | empty |
| 5 | 186 | 0.49 | 0.76 | 24 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2003 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1885 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 377 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 295 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 225 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 7OO2 · Crystal structure of an antibody targeting the capsular polysaccharide of serogroup X… · 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 7OO2 · PDBe 7OO2
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