MolNFT v1 · #47395 · protein

Mouse scavenger receptor C-type lectin carbohydrate-recognition domain.

2OX9 · Collectin placenta 1: “Mouse scavenger receptor C-type lectin carbohydrate-recognition domain.”. X-ray diffraction, 4 ligands (NAG, FUC, GAL), 4 pockets (best druggability 0.81). MolNFT v1 #47395 on GenesisL1: 3D structure, binding…

PDB: 2OX9
Type: protein
Length: 518 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Collectin placenta 1
UniProt: Q8K4Q8
Ligands: NAG, FUC, GAL, CA
Pockets: 4 · best druggability 0.81

Structure

x-ray diffraction · 3 distinct chains · 18% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Collectin placenta 1	protein	130	17% helix, 28% strand	Q8K4Q8
B	Collectin placenta 1	protein	127	19% helix, 29% strand	Q8K4Q8
C	Collectin placenta 1	protein	131	18% helix, 28% strand	Q8K4Q8

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains C
FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A, B, C, D
GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, B, C, D
CA · Calcium ion · metal · 16 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1008	0.81	0.83	84	NAG, FUC
2	196	0.51	0.77	34	empty
3	103	0.38	0.75	20	empty
4	86	0.35	0.75	23	empty

Interfaces

4 interfaces between chains.

A–C · 533 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 470 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 461 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 188 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

2OX9 · Mouse Scavenger Receptor C-type Lectin carbohydrate-recognition domain. · the same entry in another collection · chain C against C, TM-score 1.00
Q8K4Q8 · AlphaFold monomer V2.0 prediction for collectin-12 (Q8K4Q8) · a predicted model of the same protein · chain A 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 Q8K4Q8
Elsewhere: RCSB PDB 2OX9 · PDBe 2OX9 · UniProt Q8K4Q8

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