MolNFT v1 · #119835 · protein

Crystal structure of nivolumab Fab fragment

5GGQ · Nivolumab light chain: “Crystal structure of nivolumab Fab fragment”. X-ray diffraction, 7 pockets (best druggability 0.56). MolNFT v1 #119835 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5GGQ
Type: protein
Length: 419 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nivolumab light chain; Nivolumab heavy chain
Pockets: 7 · best druggability 0.56

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Nivolumab light chain	protein	211	5% helix, 51% strand	—
H	Nivolumab heavy chain	protein	208	10% helix, 50% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	419	0.56	0.73	53	empty
2	133	0.46	0.77	20	empty
3	67	0.41	0.81	21	empty
4	81	0.32	0.73	18	empty
5	60	0.32	0.76	14	empty

Interfaces

1 interface between chains.

L–H · 1589 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

5GGQ · Crystal structure of Nivolumab Fab fragment · 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
Elsewhere: RCSB PDB 5GGQ · PDBe 5GGQ

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