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Crystal structure of an anti-SARS-cov-2 human neutralizing antibody Fab fragment, C135

Analyse Crystal structure of an anti-SARS-cov-2 human neutralizing antibody Fab… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7K8R
Type: protein
Length: 434 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: C135 Fab heavy chain; C135 Fab light chain
Pockets: 4 · best druggability 0.56

Structure

x-ray diffraction · 2 distinct chains · 8% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	C135 Fab heavy chain	protein	220	10% helix, 47% strand	—
L	C135 Fab light chain	protein	214	6% helix, 50% strand	—

Ligands and binding sites

GOL · Glycerol · additive · 3 copies · chains H, L

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	370	0.56	0.75	52	empty
2	248	0.54	0.77	36	empty
3	146	0.43	0.75	24	empty
4	50	0.28	0.75	19	empty

Interfaces

1 interface between chains.

H–L · 1856 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

7K8R · Crystal structure of an anti-SARS-CoV-2 human neutralizing antibody Fab fragment, C135 · 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 7K8R · PDBe 7K8R

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