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Complex structure of antibody bd-503 and rbd-N501Y of COVID-19

Analyse Complex structure of antibody bd-503 and rbd-N501Y of COVID-19 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7EK0
Type: protein
Length: 621 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spike protein S1; Heavy chain of bd-503; Light chain of bd-503
UniProt: P0DTC2
Pockets: 5 · best druggability 0.54

Structure

x-ray diffraction · 3 distinct chains · 9% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
R	Spike protein S1	protein	193	13% helix, 28% strand	P0DTC2
H	Heavy chain of bd-503	protein	214	8% helix, 52% strand	—
L	Light chain of bd-503	protein	214	7% helix, 50% strand	—

Pockets

5 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	207	0.54	0.78	31	empty
2	318	0.53	0.74	43	empty
3	191	0.48	0.76	33	empty
4	55	0.34	0.78	15	empty
5	95	0.34	0.73	18	empty

Interfaces

3 interfaces between chains.

H–L · 1767 Å² buried · 13 hydrogen bonds · protein-protein
R–H · 773 Å² buried · 18 hydrogen bonds · protein-protein
R–L · 466 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

7EK0 · Complex Structure of antibody BD-503 and RBD-N501Y of COVID-19 · the same entry in another collection · chain R against R, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P0DTC2
Elsewhere: RCSB PDB 7EK0 · PDBe 7EK0 · UniProt P0DTC2

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