MolNFT v1 · #28754 · protein
Structure of the monomeric form of T. gondii SAG1 surface antigen bound to a human Fab
1YNT · 4F11E12 Fab variable light chain region: “Structure of the monomeric form of T. gondii SAG1 surface antigen bound to a human Fab”. X-ray diffraction, 1 ligand (CD), 20 pockets (best druggability 0.69). MolNFT v1 #28754 on GenesisL1…
- PDB
- 1YNT
- Type
- protein
- Length
- 1,427 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4F11E12 Fab variable light chain region; 4F11E12 Fab variable heavy chain region; Protein…
- UniProt
- P13664
- Ligands
- CD
- Pockets
- 20 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | 4F11E12 Fab variable light chain region | protein | 213 | 5% helix, 45% strand | — |
| B, D | 4F11E12 Fab variable heavy chain region | protein | 218 | 4% helix, 50% strand | — |
| E | Protein L | protein | 61 | 28% helix, 41% strand | — |
| F, G | Major surface antigen P30 | protein | 252 | 6% helix, 33% strand | P13664 |
Ligands and binding sites
- CD · Cadmium ion · metal · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 314 | 0.69 | 0.83 | 58 | empty |
| 2 | 75 | 0.57 | 0.88 | 25 | empty |
| 3 | 72 | 0.56 | 0.88 | 24 | empty |
| 4 | 311 | 0.52 | 0.74 | 49 | empty |
| 5 | 93 | 0.51 | 0.83 | 19 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1916 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1913 Ų buried · 18 hydrogen bonds · protein-protein
- A–E · 831 Ų buried · 12 hydrogen bonds · protein-protein
- C–E · 694 Ų buried · 9 hydrogen bonds · protein-protein
- B–F · 605 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 disulfide (disulfide).
Compared structures
- 1YNT · Structure of the monomeric form of T. gondii SAG1 surface antigen bound to a human Fab · the same entry in another collection · chain G against G, TM-score 1.00
- P13664 · AlphaFold monomer V2.0 prediction for major surface antigen P30 (P13664) · a predicted model of the same protein · chain F against A, TM-score 0.55
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 P13664
- Elsewhere: RCSB PDB 1YNT · PDBe 1YNT · UniProt P13664
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