MolNFT v1 · #128786 · protein

Co-crystal structure of a cross-reactive bactericidal human antibody targeting meningococcal vaccine antigen factor H binding protein

5O14 · Factor H binding protein variant 1.1: “Co-crystal structure of a cross-reactive bactericidal human antibody targeting meningococcal vaccine antigen…”. X-ray diffraction, 1 ligand (CL), 12 pockets (best druggability 0.63). MolNFT v1…

PDB: 5O14
Type: protein
Length: 1,331 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Factor H binding protein variant 1.1; Fab 1A12 heavy chain; Fab 1A12 light chain
UniProt: Q9JXV4
Ligands: CL
Pockets: 12 · best druggability 0.63

Structure

x-ray diffraction · 6 distinct chains · 7% helix, 54% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Factor H binding protein variant 1.1	protein	229	7% helix, 61% strand	Q9JXV4
B	Factor H binding protein variant 1.1	protein	231	6% helix, 60% strand	Q9JXV4
C	Fab 1A12 heavy chain	protein	223	9% helix, 51% strand	—
D	Fab 1A12 light chain	protein	215	7% helix, 51% strand	—
L	Fab 1A12 light chain	protein	212	6% helix, 51% strand	—
H	Fab 1A12 heavy chain	protein	221	8% helix, 51% strand	—

Ligands and binding sites

CL · Chloride ion · ion · 2 copies · chains C, D, L, H
EDO · 1,2-ethanediol · additive · 3 copies · chains A, H

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

Pockets

12 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	629	0.63	0.74	63	empty
2	634	0.63	0.74	64	empty
3	275	0.55	0.76	40	empty
4	177	0.54	0.79	39	empty
5	144	0.53	0.80	26	empty

Interfaces

8 interfaces between chains.

C–D · 1888 Å² buried · 14 hydrogen bonds · protein-protein
L–H · 1809 Å² buried · 11 hydrogen bonds · protein-protein
A–H · 647 Å² buried · 19 hydrogen bonds · protein-protein
B–C · 642 Å² buried · 16 hydrogen bonds · protein-protein
A–D · 329 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

5O14 · Co-crystal structure of a cross-reactive bactericidal human antibody targeting… · 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 Q9JXV4
Elsewhere: RCSB PDB 5O14 · PDBe 5O14 · UniProt Q9JXV4

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