MolNFT v1 · #116870 · protein

Crystal structure of the sclerostin-neutralizing Fab ABD09097

5DR5 · ABD09097 Fab heavy chain: “Crystal structure of the sclerostin-neutralizing Fab ABD09097”. X-ray diffraction, 7 pockets (best druggability 0.59). MolNFT v1 #116870 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5DR5
Type: protein
Length: 439 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ABD09097 Fab heavy chain; ABD09097 Fab light chain
Pockets: 7 · best druggability 0.59

Structure

x-ray diffraction · 2 distinct chains · 8% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	ABD09097 Fab heavy chain	protein	224	9% helix, 48% strand	—
L	ABD09097 Fab light chain	protein	215	6% helix, 53% strand	—

Pockets

7 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	476	0.59	0.74	48	empty
2	54	0.53	0.89	21	empty
3	156	0.52	0.79	28	empty
4	125	0.45	0.77	19	empty
5	79	0.31	0.74	23	empty

Interfaces

1 interface between chains.

H–L · 1898 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5DR5 · Crystal structure of the sclerostin-neutralizing Fab AbD09097 · the same entry in another collection · chain H against H, 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
Elsewhere: RCSB PDB 5DR5 · PDBe 5DR5

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