MolNFT v1 · #182817 · protein

Cryo-EM structure of broadly neutralizing antibody 2-36 in complex with prefusion SARS-cov-2 spike glycoprotein

7N5H: “Cryo-EM structure of broadly neutralizing antibody 2-36 in complex with prefusion SARS-cov-2 spike…”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.86). MolNFT v1 #182817 on GenesisL1: 3D structure, binding…

PDB: 7N5H
Type: protein
Length: 3,739 residues
Chains: 9
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spike glycoprotein; 2-36 Fab heavy chain; 2-36 Fab light chain
UniProt: P0DTC2
Ligands: NAG
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 5 distinct chains · 21% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Spike glycoprotein	protein	1011	22% helix, 32% strand	P0DTC2
B	Spike glycoprotein	protein	1013	23% helix, 33% strand	P0DTC2
C	Spike glycoprotein	protein	1010	22% helix, 32% strand	P0DTC2
H, E, J	2-36 Fab heavy chain	protein	128	7% helix, 45% strand	—
L, F, K	2-36 Fab light chain	protein	107	3% helix, 50% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 41 copies · chains A, B, C

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1146	0.86	0.87	125	empty
2	843	0.86	0.88	112	empty
3	549	0.80	0.86	44	empty
4	857	0.76	0.80	109	empty
5	616	0.73	0.80	48	empty

Interfaces

14 interfaces between chains.

B–C · 4401 Å² buried · 41 hydrogen bonds · protein-protein
A–B · 4386 Å² buried · 37 hydrogen bonds · protein-protein
A–C · 4246 Å² buried · 33 hydrogen bonds · protein-protein
H–L · 890 Å² buried · 8 hydrogen bonds · protein-protein
J–K · 890 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 45 disulfide, 25 glycan (disulfide, N-glycosylation).

Compared structures

7N5H · Cryo-EM structure of broadly neutralizing antibody 2-36 in complex with prefusion… · the same entry in another collection · chain A against A, 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 P0DTC2
Elsewhere: RCSB PDB 7N5H · PDBe 7N5H · UniProt P0DTC2

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