MolNFT v1 · #114322 · protein

Crystal structure of the anti-circumsporozoite protein 663 germline antibody

5BK5 · 663 germline antibody, heavy chain: “Crystal structure of the anti-circumsporozoite protein 663 germline antibody”. X-ray diffraction, 20 pockets (best druggability 0.79). MolNFT v1 #114322 on GenesisL1: 3D structure, binding sites…

PDB: 5BK5
Type: protein
Length: 1,723 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 663 germline antibody, heavy chain; 663 germline antibody, light chain
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 7 distinct chains · 5% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	663 germline antibody, heavy chain	protein	216	3% helix, 51% strand	—
H	663 germline antibody, heavy chain	protein	211	3% helix, 53% strand	—
A	663 germline antibody, light chain	protein	219	5% helix, 50% strand	—
G, C	663 germline antibody, light chain	protein	217	6% helix, 50% strand	—
D	663 germline antibody, heavy chain	protein	213	4% helix, 53% strand	—
F	663 germline antibody, heavy chain	protein	213	6% helix, 51% strand	—
E	663 germline antibody, light chain	protein	217	6% helix, 50% strand	—

Ligands and binding sites

GOL · Glycerol · additive · 14 copies · chains B, D, A, H, G, F, C, E

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

Pockets

20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1100	0.79	0.81	112	GOL
2	580	0.76	0.83	79	GOL
3	475	0.71	0.81	47	empty
4	445	0.70	0.81	44	empty
5	331	0.63	0.80	57	empty

Interfaces

19 interfaces between chains.

B–A · 1825 Å² buried · 17 hydrogen bonds · protein-protein
H–G · 1786 Å² buried · 18 hydrogen bonds · protein-protein
D–C · 1769 Å² buried · 19 hydrogen bonds · protein-protein
F–E · 1736 Å² buried · 14 hydrogen bonds · protein-protein
H–F · 1019 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

5BK5 · Crystal structure of the anti-circumsporozoite protein 663 germline antibody · the same entry in another collection · chain B against B, 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 5BK5 · PDBe 5BK5

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