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Crystal structure of the human neutralizing antibody Fab fragment T025 bound to tbev ediii (western subtype)

Analyse Crystal structure of the human neutralizing antibody Fab fragment T025 bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7LSF
Type: protein
Length: 525 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: T025 Fab heavy chain; T025 Fab light chain; Envelope protein E
UniProt: E3UMN9
Ligands: NA
Pockets: 3 · best druggability 0.61

Structure

x-ray diffraction · 3 distinct chains · 6% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	T025 Fab heavy chain	protein	218	8% helix, 49% strand	—
L	T025 Fab light chain	protein	213	6% helix, 51% strand	—
E	Envelope protein E	protein	94	0% helix, 57% strand	E3UMN9

Ligands and binding sites

NA · Sodium ion · metal · 2 copies · chains H, L, E
GOL · Glycerol · additive · chains H, L

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	527	0.61	0.75	58	empty
2	81	0.34	0.75	22	NA
3	81	0.31	0.73	19	empty

Interfaces

3 interfaces between chains.

H–L · 1812 Å² buried · 16 hydrogen bonds · protein-protein
H–E · 386 Å² buried · 10 hydrogen bonds · protein-protein
L–E · 299 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

7LSF · Crystal structure of the human neutralizing antibody Fab fragment T025 bound to TBEV… · the same entry in another collection · chain H against H, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt E3UMN9
Elsewhere: RCSB PDB 7LSF · PDBe 7LSF · UniProt E3UMN9

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