Research workbench
N-acetylgalactosamine binding mutant of mannose-binding protein a (qpdwg-hdrpy), complex with N-acetylgalactosamine
Analyse N-acetylgalactosamine binding mutant of mannose-binding protein a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1FIH
- Type
- protein
- Length
- 462 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mannose-binding protein a
- UniProt
- P19999
- Ligands
- NGA, CA, CL
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Mannose-binding protein a | protein | 154 | 32% helix, 23% strand | P19999 |
Ligands and binding sites
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 4 copies · chains A, B, C
- CA · Calcium ion · metal · 9 copies · chains A, B, C
- CL · Chloride ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 947 | 0.72 | 0.76 | 83 | NGA |
| 2 | 234 | 0.56 | 0.78 | 31 | empty |
| 3 | 221 | 0.54 | 0.77 | 27 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1128 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 1033 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 1033 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1FIH · N-acetylgalactosamine binding mutant of mannose-binding protein a (qpdwg-hdrpy), complex… · 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 0.96
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 1FIH · PDBe 1FIH · UniProt P19999
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