MolNFT v1 · #137195 · protein

Crystal structure of Fab fragment of anti-tnfa antibody infliximab in an I-centered orthorhombic crystal form

5VH4 · Infliximab Fab heavy chain: “Crystal structure of Fab fragment of anti-tnfa antibody infliximab in an I-centered orthorhombic crystal form”. X-ray diffraction, 1 ligand (NAD), 11 pockets (best druggability 0.71). MolNFT v1 #137195…

PDB: 5VH4
Type: protein
Length: 868 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Infliximab Fab heavy chain; Infliximab Fab light chain
Ligands: NAD
Pockets: 11 · best druggability 0.71

Structure

x-ray diffraction · 3 distinct chains · 8% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Infliximab Fab heavy chain	protein	222	9% helix, 52% strand	—
L, B	Infliximab Fab light chain	protein	213	6% helix, 51% strand	—
A	Infliximab Fab heavy chain	protein	220	10% helix, 53% strand	—

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains H, A
EDO · 1,2-ethanediol · additive · 5 copies · chains H, L, A, B

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

Pockets

11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	411	0.71	0.82	45	empty
2	592	0.71	0.80	47	empty
3	659	0.68	0.76	83	EDO
4	350	0.58	0.76	52	empty
5	68	0.50	0.85	21	empty

Interfaces

5 interfaces between chains.

H–L · 1760 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 1747 Å² buried · 16 hydrogen bonds · protein-protein
L–B · 983 Å² buried · 16 hydrogen bonds · protein-protein
L–A · 213 Å² buried · 4 hydrogen bonds · protein-protein
H–B · 199 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

5VH4 · Crystal structure of Fab fragment of anti-TNFa antibody infliximab in an I-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 5VH4 · PDBe 5VH4

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.