MolNFT v1 · #137810 · protein

Crystal structure of crenezumab Fab in complex with abeta

5VZY · Crenezumab Fab heavy CHAIN,IMMUNOGLOBULIN gamma-1 heavy…: “Crystal structure of crenezumab Fab in complex with abeta”. X-ray diffraction, 4 pockets (best druggability 0.50). MolNFT v1 #137810 on GenesisL1: 3D structure, binding…

PDB: 5VZY
Type: protein
Length: 436 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Crenezumab Fab heavy CHAIN,IMMUNOGLOBULIN gamma-1 heavy chain; Crenezumab Fab light…
UniProt: P0DOX5, Q0KKI6, P05067
Pockets: 4 · best druggability 0.50

Structure

x-ray diffraction · 3 distinct chains · 6% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Crenezumab Fab heavy CHAIN,IMMUNOGLOBULIN gamma-1 heavy chain	protein	206	7% helix, 51% strand	P0DOX5
L	Crenezumab Fab light CHAIN,IMMUNOBLOBULIN light chain	protein	218	6% helix, 50% strand	Q0KKI6
A	Amyloid beta A4 protein	protein	12	0% helix, 0% strand	P05067

Pockets

4 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	240	0.50	0.75	40	empty
2	155	0.45	0.76	27	empty
3	123	0.36	0.73	26	empty
4	70	0.30	0.74	16	empty

Interfaces

3 interfaces between chains.

H–L · 1516 Å² buried · 10 hydrogen bonds · protein-protein
H–A · 535 Å² buried · 7 hydrogen bonds · protein-protein
L–A · 467 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5VZY · Crystal structure of crenezumab Fab in complex with Abeta · the same entry in another collection · chain H against H, TM-score 1.00
P05067 · AlphaFold monomer V2.0 prediction for amyloid-beta precursor protein (P05067) · a predicted model of the same protein · chain A against A, TM-score 0.29

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 P0DOX5
Every structure of UniProt Q0KKI6
Every structure of UniProt P05067
Elsewhere: RCSB PDB 5VZY · PDBe 5VZY · UniProt P0DOX5 · UniProt Q0KKI6 · UniProt P05067

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