MolNFT v1 · #74211 · protein
Crystal structure of trans-sialidase in complex with the Fab fragment of a neutralizing monoclonal IgG antibody
3OPZ: “Crystal structure of trans-sialidase in complex with the Fab fragment of a neutralizing monoclonal IgG…”. X-ray diffraction, 1 ligand (NA), 20 pockets (best druggability 0.77). MolNFT v1 #74211 on GenesisL1: 3D structure, binding…
- PDB
- 3OPZ
- Type
- protein
- Length
- 3,172 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trans-sialidase; Heavy chain of the Fab fragment of immunoglobulin G; Light chain of the…
- EC
- 3.2.1.18
- UniProt
- Q26966
- Ligands
- NA
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Trans-sialidase (EC 3.2.1.18) | protein | 625 | 7% helix, 48% strand | Q26966 |
| H | Heavy chain of the Fab fragment of immunoglobulin G | protein | 220 | 7% helix, 50% strand | — |
| I | Heavy chain of the Fab fragment of immunoglobulin G | protein | 220 | 5% helix, 52% strand | — |
| J | Heavy chain of the Fab fragment of immunoglobulin G | protein | 221 | 5% helix, 51% strand | — |
| L, M, N | Light chain of the Fab fragment of immunoglobulin G | protein | 212 | 8% helix, 52% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 851 | 0.77 | 0.80 | 62 | DIO |
| 2 | 811 | 0.76 | 0.80 | 61 | DIO |
| 3 | 831 | 0.76 | 0.80 | 59 | empty |
| 4 | 272 | 0.59 | 0.78 | 29 | empty |
| 5 | 237 | 0.58 | 0.79 | 30 | empty |
Interfaces
12 interfaces between chains.
- J–N · 1952 Ų buried · 16 hydrogen bonds · protein-protein
- I–M · 1922 Ų buried · 16 hydrogen bonds · protein-protein
- H–L · 1908 Ų buried · 11 hydrogen bonds · protein-protein
- C–J · 565 Ų buried · 14 hydrogen bonds · protein-protein
- A–H · 560 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide (disulfide).
Compared structures
- 3OPZ · Crystal structure of trans-sialidase in complex with the Fab fragment of a neutralizing… · 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
- Every structure of UniProt Q26966
- Elsewhere: RCSB PDB 3OPZ · PDBe 3OPZ · UniProt Q26966
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