MolNFT v1 · #137309 · protein

Crystal structure of Fab fragment of anti-CD22 epratuzumab

5VKK · Epratuzumab Fab heavy chain: “Crystal structure of Fab fragment of anti-CD22 epratuzumab”. X-ray diffraction, 8 pockets (best druggability 0.71). MolNFT v1 #137309 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5VKK
Type: protein
Length: 871 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Epratuzumab Fab heavy chain; Epratuzumab Fab light chain
UniProt: Q6N089, Q8TCD0
Pockets: 8 · best druggability 0.71

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Epratuzumab Fab heavy chain	protein	218	8% helix, 52% strand	Q6N089
L, B	Epratuzumab Fab light chain	protein	219	6% helix, 51% strand	Q8TCD0
A	Epratuzumab Fab heavy chain	protein	215	8% helix, 52% strand	Q6N089

Pockets

8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1005	0.71	0.75	120	empty
2	344	0.56	0.75	47	empty
3	193	0.45	0.74	28	empty
4	67	0.33	0.75	14	empty
5	61	0.33	0.76	16	empty

Interfaces

4 interfaces between chains.

A–B · 1997 Å² buried · 15 hydrogen bonds · protein-protein
H–L · 1957 Å² buried · 15 hydrogen bonds · protein-protein
L–A · 248 Å² buried · 2 hydrogen bonds · protein-protein
L–B · 161 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide (disulfide).

Compared structures

5VKK · Crystal structure of Fab fragment of anti-CD22 Epratuzumab · 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
Every structure of UniProt Q6N089
Every structure of UniProt Q8TCD0
Elsewhere: RCSB PDB 5VKK · PDBe 5VKK · UniProt Q6N089 · UniProt Q8TCD0

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