Research workbench

Mouse ecd with FAB1

Analyse Mouse ecd with FAB1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6O9H
Type: protein
Length: 1,034 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Heavy chain; Light chain; Gastric inhibitory polypeptide receptor
UniProt: Q0P543
Ligands: NA
Pockets: 11 · best druggability 0.81

Structure

x-ray diffraction · 5 distinct chains · 8% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Heavy chain	protein	213	6% helix, 53% strand	—
L	Light chain	protein	214	6% helix, 53% strand	—
A	Heavy chain	protein	210	6% helix, 53% strand	—
B	Light chain	protein	217	5% helix, 52% strand	—
D, C	Gastric inhibitory polypeptide receptor	protein	90	28% helix, 24% strand	Q0P543

Ligands and binding sites

NA · Sodium ion · metal · 2 copies · chains A, C, H, D

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

Pockets

11 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	928	0.81	0.83	95	empty
2	737	0.75	0.80	70	empty
3	1138	0.74	0.77	126	empty
4	138	0.49	0.78	19	empty
5	74	0.47	0.83	22	empty

Interfaces

9 interfaces between chains.

H–L · 1875 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 1794 Å² buried · 15 hydrogen bonds · protein-protein
H–B · 785 Å² buried · 12 hydrogen bonds · protein-protein
H–D · 560 Å² buried · 16 hydrogen bonds · protein-protein
A–C · 515 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 disulfide (disulfide).

Compared structures

6O9H · Mouse ECD with Fab1 · the same entry in another collection · chain C against C, TM-score 1.00
Q0P543 · AlphaFold monomer V2.0 prediction for gastric inhibitory polypeptide receptor (Q0P543) · a predicted model of the same protein · chain C against A, TM-score 0.97

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 Q0P543
Elsewhere: RCSB PDB 6O9H · PDBe 6O9H · UniProt Q0P543

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