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Crystal structure of Fab fragment of the anti-tnfa antibody infliximab in a C-centered orthorhombic crystal form

Analyse Crystal structure of Fab fragment of the anti-tnfa antibody infliximab in a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5VH3
Type: protein
Length: 864 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Infliximab Fab heavy chain; Infliximab Fab light chain
Pockets: 8 · best druggability 0.73

Structure

x-ray diffraction · 2 distinct chains · 8% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H, A	Infliximab Fab heavy chain	protein	218	11% helix, 53% strand	—
L, B	Infliximab Fab light chain	protein	214	6% helix, 50% strand	—

Ligands and binding sites

EDO · 1,2-ethanediol · additive · chains B

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

Pockets

8 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	451	0.73	0.83	67	empty
2	303	0.61	0.79	43	empty
3	322	0.58	0.77	41	empty
4	63	0.56	0.89	20	empty
5	64	0.53	0.87	21	empty

Interfaces

5 interfaces between chains.

A–B · 1704 Å² buried · 14 hydrogen bonds · protein-protein
H–L · 1650 Å² buried · 13 hydrogen bonds · protein-protein
L–B · 1137 Å² buried · 8 hydrogen bonds · protein-protein
L–A · 11 Å² buried · 0 hydrogen bonds · protein-protein
H–B · 11 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

5VH3 · Crystal structure of Fab fragment of the anti-TNFa antibody infliximab in a C-centered… · 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 5VH3 · PDBe 5VH3

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