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Structure of the 6TH type III domain from human fibronectin

Analyse Structure of the 6TH type III domain from human fibronectin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6MSV
Type: protein
Length: 1,015 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fibronectin
UniProt: P02751
Pockets: 11 · best druggability 0.85

Structure

x-ray diffraction · 7 distinct chains · 0% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Fibronectin	protein	86	0% helix, 52% strand	P02751
B, G, J, L	Fibronectin	protein	83	0% helix, 53% strand	P02751
C	Fibronectin	protein	85	0% helix, 51% strand	P02751
D	Fibronectin	protein	90	0% helix, 49% strand	P02751
E, F, K	Fibronectin	protein	84	0% helix, 52% strand	P02751
H	Fibronectin	protein	89	0% helix, 48% strand	P02751
I	Fibronectin	protein	81	0% helix, 56% strand	P02751

Ligands and binding sites

GOL · Glycerol · additive · 2 copies · chains B, L, F

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

Pockets

11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1163	0.85	0.86	116	empty
2	270	0.69	0.85	44	empty
3	86	0.68	0.93	29	empty
4	676	0.66	0.75	58	GOL
5	134	0.66	0.89	24	empty

Interfaces

26 interfaces between chains.

E–K · 792 Å² buried · 11 hydrogen bonds · protein-protein
A–J · 754 Å² buried · 15 hydrogen bonds · protein-protein
G–H · 752 Å² buried · 12 hydrogen bonds · protein-protein
C–I · 743 Å² buried · 12 hydrogen bonds · protein-protein
B–L · 733 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

6MSV · Structure of the 6th type III domain from human fibronectin · the same entry in another collection · chain L against L, TM-score 1.00

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 P02751
Elsewhere: RCSB PDB 6MSV · PDBe 6MSV · UniProt P02751

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