Research workbench

Crystal structure of 4493 Fab in complex with circumsporozoite protein npdp and anti-kappa vhh domain

Analyse Crystal structure of 4493 Fab in complex with circumsporozoite protein npdp and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6O29
Type: protein
Length: 1,140 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 4493 Fab heavy chain; 4493 kappa light chain; Circumsporozoite protein; Anti-kappa vhh…
UniProt: P02893
Pockets: 15 · best druggability 0.68

Structure

x-ray diffraction · 6 distinct chains · 7% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	4493 Fab heavy chain	protein	217	7% helix, 52% strand	—
B, L	4493 kappa light chain	protein	214	7% helix, 50% strand	—
H	4493 Fab heavy chain	protein	223	9% helix, 51% strand	—
C	Circumsporozoite protein	protein	15	0% helix, 0% strand	P02893
D	Circumsporozoite protein	protein	15	0% helix, 0% strand	P02893
K, E	Anti-kappa vhh domain	protein	121	7% helix, 50% strand	—

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, K

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

Pockets

15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	69	0.68	0.95	27	empty
2	560	0.67	0.77	83	empty
3	97	0.65	0.91	32	empty
4	485	0.63	0.76	68	empty
5	126	0.58	0.84	29	empty

Interfaces

14 interfaces between chains.

H–L · 1943 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 1738 Å² buried · 15 hydrogen bonds · protein-protein
L–E · 610 Å² buried · 7 hydrogen bonds · protein-protein
B–K · 605 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 471 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide (disulfide).

Compared structures

6O29 · Crystal structure of 4493 Fab in complex with circumsporozoite protein NPDP and… · the same entry in another collection · chain E against E, TM-score 1.00
P02893 · AlphaFold monomer V2.0 prediction for circumsporozoite protein (P02893) · a predicted model of the same protein · chain C against A, TM-score 0.30

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 P02893
Elsewhere: RCSB PDB 6O29 · PDBe 6O29 · UniProt P02893

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.