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MERS-cov S complex with human neutralizing LCA60 antibody Fab fragment (state 2)

Analyse MERS-cov S complex with human neutralizing LCA60 antibody Fab fragment (state 2) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6NB4
Type: protein
Length: 3,315 residues
Chains: 5
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spike glycoprotein; LCA60 heavy chain; LCA60 light chain
UniProt: A0A140AYW5
Ligands: NAG, MAN, BMA
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 5 distinct chains · 20% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Spike glycoprotein	protein	1169	20% helix, 32% strand	A0A140AYW5
B	Spike glycoprotein	protein	958	22% helix, 33% strand	A0A140AYW5
C	Spike glycoprotein	protein	959	22% helix, 31% strand	A0A140AYW5
H	LCA60 heavy chain	protein	123	10% helix, 50% strand	—
L	LCA60 light chain	protein	106	8% helix, 41% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 85 copies · chains A, B, H, C
MAN · alpha-D-mannopyranose · sugar · 17 copies · chains B, H, C, A
BMA · beta-D-mannopyranose · sugar · 11 copies · chains A, B, H, 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	1024	0.87	0.88	120	empty
2	889	0.85	0.87	94	empty
3	1188	0.83	0.84	117	empty
4	846	0.83	0.85	78	empty
5	660	0.81	0.86	89	empty

Interfaces

6 interfaces between chains.

A–B · 5011 Å² buried · 62 hydrogen bonds · protein-protein
A–C · 4247 Å² buried · 54 hydrogen bonds · protein-protein
B–C · 4089 Å² buried · 54 hydrogen bonds · protein-protein
H–L · 731 Å² buried · 3 hydrogen bonds · protein-protein
A–L · 408 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 47 glycan, 45 disulfide (N-glycosylation, disulfide).

Compared structures

6NB4 · MERS-CoV S complex with human neutralizing LCA60 antibody Fab fragment (state 2) · 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 A0A140AYW5
Elsewhere: RCSB PDB 6NB4 · PDBe 6NB4 · UniProt A0A140AYW5

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