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Structure of MERS-coronavirus spike receptor-binding domain (ENGLAND1 strain) in complex with vaccine-elicited murine neutralizing antibody D12 (crystal form 2)

Analyse Structure of MERS-coronavirus spike receptor-binding domain (ENGLAND1 strain)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4ZPV
Type: protein
Length: 1,265 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: D12 Fab heavy chain; D12 Fab light chain; Spike glycoprotein
UniProt: K9N5Q8
Ligands: NAG
Pockets: 18 · best druggability 0.76

Structure

x-ray diffraction · 4 distinct chains · 11% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H, A	D12 Fab heavy chain	protein	213	6% helix, 50% strand	—
L, B	D12 Fab light chain	protein	212	6% helix, 50% strand	—
S	Spike glycoprotein	protein	207	16% helix, 31% strand	K9N5Q8
R	Spike glycoprotein	protein	208	16% helix, 37% strand	K9N5Q8

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains R

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

Pockets

18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	957	0.76	0.79	91	empty
2	998	0.76	0.78	91	empty
3	163	0.69	0.88	35	empty
4	255	0.68	0.84	47	empty
5	274	0.64	0.81	29	empty

Interfaces

10 interfaces between chains.

B–A · 1747 Å² buried · 10 hydrogen bonds · protein-protein
H–L · 1727 Å² buried · 10 hydrogen bonds · protein-protein
S–B · 621 Å² buried · 5 hydrogen bonds · protein-protein
L–R · 574 Å² buried · 4 hydrogen bonds · protein-protein
H–R · 547 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

4ZPV · Structure of MERS-Coronavirus Spike Receptor-binding Domain (England1 Strain) in Complex… · 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 K9N5Q8
Elsewhere: RCSB PDB 4ZPV · PDBe 4ZPV · UniProt K9N5Q8

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