Research workbench
Yb substituted subtilisin fragment of mannose binding protein-a (sub- mbp-a), mad structure at 110K
Analyse Yb substituted subtilisin fragment of mannose binding protein-a (sub- mbp-a)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YTT
- Type
- protein
- Length
- 227 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mannose-binding protein a
- UniProt
- P19999
- Ligands
- YB
- Pockets
- 1 · best druggability 0.37
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mannose-binding protein a | protein | 115 | 21% helix, 33% strand | P19999 |
| B | Mannose-binding protein a | protein | 112 | 21% helix, 27% strand | P19999 |
Ligands and binding sites
- YB · Ytterbium (III) ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 94 | 0.37 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 674 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1YTT · Yb substituted subtilisin fragment of mannose binding protein-a (sub-mbp-a), mad… · the same entry in another collection · chain A against A, TM-score 1.00
- P19999 · AlphaFold monomer V2.0 prediction for mannose-binding protein a (P19999) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P19999
- Elsewhere: RCSB PDB 1YTT · PDBe 1YTT · UniProt P19999
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