Research workbench
Mannose-binding protein-a mutant (qpdwgh) complexed with N-acetyl-D- galactosamine
Analyse Mannose-binding protein-a mutant (qpdwgh) complexed with N-acetyl-D… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1BCH
- 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, A2G, CA, NA, CL
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1, 2, 3 | Mannose-binding protein-a | protein | 154 | 32% helix, 25% strand | P19999 |
Ligands and binding sites
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 2 copies · chains 2, 3
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · chains 1
- CA · Calcium ion · metal · 9 copies · chains 1, 2, 3
- NA · Sodium ion · metal · chains 1, 2, 3
- CL · Chloride ion · ion · 3 copies · chains 1, 2, 3
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 642 | 0.65 | 0.75 | 61 | empty |
| 2 | 210 | 0.51 | 0.76 | 25 | empty |
| 3 | 210 | 0.51 | 0.76 | 28 | empty |
| 4 | 183 | 0.50 | 0.76 | 26 | empty |
Interfaces
3 interfaces between chains.
- 1–2 · 1123 Ų buried · 10 hydrogen bonds · protein-protein
- 1–3 · 1043 Ų buried · 8 hydrogen bonds · protein-protein
- 2–3 · 1029 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1BCH · Mannose-binding protein-a mutant (qpdwgh) complexed with N-acetyl-D-galactosamine · the same entry in another collection · chain 1 against 1, TM-score 1.00
- P19999 · AlphaFold monomer V2.0 prediction for mannose-binding protein a (P19999) · a predicted model of the same protein · chain 1 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 1BCH · PDBe 1BCH · UniProt P19999
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