MolNFT v1 · #20398 · protein
Mannose-binding protein, subtilisin digest fragment complex with alpha-methyl-D-mannopyranoside (1.3 M)
1RDM · Mannose-binding protein-C: “Mannose-binding protein, subtilisin digest fragment complex with alpha-methyl-D-mannopyranoside (1.3 M)”. X-ray diffraction, 3 ligands (MMA, CA, CL), 1 pocket (best druggability 0.33). MolNFT v1 #20398 on…
- PDB
- 1RDM
- Type
- protein
- Length
- 223 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mannose-binding protein-C
- UniProt
- P08661
- Ligands
- MMA, CA, CL
- Pockets
- 1 · best druggability 0.33
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | Mannose-binding protein-C | protein | 111 | 18% helix, 29% strand | P08661 |
| 2 | Mannose-binding protein-C | protein | 112 | 18% helix, 29% strand | P08661 |
Ligands and binding sites
- MMA · methyl alpha-D-mannopyranoside · sugar · 3 copies · chains 1, 2
- CA · Calcium ion · metal · 4 copies · chains 1, 2
- CL · Chloride ion · ion · chains 1
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 | 86 | 0.33 | 0.73 | 12 | empty |
Interfaces
1 interface between chains.
- 1–2 · 707 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1RDM · Mannose-binding protein, subtilisin digest fragment complex with… · the same entry in another collection · chain 1 against 1, TM-score 1.00
- P08661 · AlphaFold monomer V2.0 prediction for mannose-binding protein C (P08661) · a predicted model of the same protein · chain 1 against A, TM-score 0.99
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 P08661
- Elsewhere: RCSB PDB 1RDM · PDBe 1RDM · UniProt P08661
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