MolNFT v1 · #20400 · protein

Mannose-binding protein, subtilisin digest fragment

1RDO · Mannose-binding protein-C: “Mannose-binding protein, subtilisin digest fragment”. X-ray diffraction, 2 ligands (CA, CL), 1 pocket (best druggability 0.31). MolNFT v1 #20400 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 1RDO
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: CA, CL
Pockets: 1 · best druggability 0.31

Structure

x-ray diffraction · 2 distinct chains · 18% helix, 31% 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, 34% strand	P08661

Ligands and binding sites

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	81	0.31	0.73	11	empty

Interfaces

1 interface between chains.

1–2 · 695 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

1RDO · Mannose-binding protein, subtilisin digest fragment · 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 1RDO · PDBe 1RDO · UniProt P08661

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