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Crystal structure of human chondroadherin

Analyse Crystal structure of human chondroadherin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5LFN
Type: protein
Length: 1,296 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Chondroadherin
UniProt: O15335
Ligands: CL
Pockets: 5 · best druggability 0.82

Structure

x-ray diffraction · 3 distinct chains · 8% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Chondroadherin	protein	324	8% helix, 17% strand	O15335
C	Chondroadherin	protein	323	8% helix, 18% strand	O15335
D	Chondroadherin	protein	325	8% helix, 17% strand	O15335

Ligands and binding sites

CL · Chloride ion · ion · 2 copies · chains B, C

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

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1192	0.82	0.83	113	empty
2	978	0.81	0.82	97	empty
3	148	0.51	0.80	24	empty
4	138	0.43	0.76	28	empty
5	57	0.38	0.80	15	empty

Interfaces

4 interfaces between chains.

C–D · 1069 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 870 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 453 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 134 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 disulfide (disulfide).

Compared structures

5LFN · Crystal structure of human chondroadherin · the same entry in another collection · chain D against D, TM-score 1.00
O15335 · AlphaFold monomer V2.0 prediction for chondroadherin (O15335) · a predicted model of the same protein · chain C 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 O15335
Elsewhere: RCSB PDB 5LFN · PDBe 5LFN · UniProt O15335

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