MolNFT v1 · #149354 · protein

Crystal structure of a V2P-reactive RV144 vaccine-like antibody, CAP228-16H, in complex with a heterologous CAP225 V1V2

6FY2 · CAP228-16H heavy chain: “Crystal structure of a V2P-reactive RV144 vaccine-like antibody, CAP228-16H, in complex with a heterologous…”. X-ray diffraction, 1 ligand (SO4), 8 pockets (best druggability 0.72). MolNFT v1 #149354 on…

PDB: 6FY2
Type: protein
Length: 900 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CAP228-16H heavy chain; CAP228-16H light chain; CAP225 scaffolded V1V2
Ligands: SO4
Pockets: 8 · best druggability 0.72

Structure

x-ray diffraction · 3 distinct chains · 9% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H, X	CAP228-16H heavy chain	protein	219	7% helix, 53% strand	—
L, Y	CAP228-16H light chain	protein	209	8% helix, 51% strand	—
P, Z	CAP225 scaffolded V1V2	protein	22	41% helix, 0% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 3 copies · chains H, P, X, Z
GOL · Glycerol · additive · 4 copies · chains L, H, Y

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

Pockets

8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	379	0.72	0.83	43	empty
2	584	0.63	0.75	58	empty
3	574	0.62	0.74	56	GOL
4	165	0.44	0.75	28	empty
5	94	0.43	0.79	23	empty

Interfaces

9 interfaces between chains.

H–L · 1718 Å² buried · 12 hydrogen bonds · protein-protein
X–Y · 1705 Å² buried · 12 hydrogen bonds · protein-protein
H–P · 526 Å² buried · 10 hydrogen bonds · protein-protein
X–Z · 496 Å² buried · 10 hydrogen bonds · protein-protein
H–X · 428 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

6FY2 · Crystal structure of a V2p-reactive RV144 vaccine-like antibody, CAP228-16H, 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
Elsewhere: RCSB PDB 6FY2 · PDBe 6FY2

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