MolNFT v1 · #183847 · protein

M971 Fab in complex with anti-kappa vhh domain

7O4Y: “M971 Fab in complex with anti-kappa vhh domain”. X-ray diffraction, 7 pockets (best druggability 0.72). MolNFT v1 #183847 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7O4Y
Type: protein
Length: 553 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Anti-kappa vhh domain; M971 Fab heavy chain; M971 Fab light chain
Pockets: 7 · best druggability 0.72

Structure

x-ray diffraction · 3 distinct chains · 6% helix, 53% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
K	Anti-kappa vhh domain	protein	120	5% helix, 50% strand	—
H	M971 Fab heavy chain	protein	219	7% helix, 56% strand	—
L	M971 Fab light chain	protein	214	6% helix, 51% 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	320	0.72	0.85	64	empty
2	279	0.56	0.77	46	empty
3	219	0.51	0.76	30	empty
4	110	0.38	0.75	22	empty
5	68	0.35	0.76	23	empty

Interfaces

3 interfaces between chains.

H–L · 1636 Å² buried · 15 hydrogen bonds · protein-protein
K–H · 285 Å² buried · 4 hydrogen bonds · protein-protein
K–L · 242 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

7O4Y · m971 Fab in complex with anti-Kappa VHH domain · the same entry in another collection · chain K against K, 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 7O4Y · PDBe 7O4Y

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