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Structure of an anti-hel Fab fragment complexed with bobwhite quail lysozyme

Analyse Structure of an anti-hel Fab fragment complexed with bobwhite quail lysozyme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1BQL
Type: protein
Length: 555 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hyhel-5 Fab (light chain); Hyhel-5 Fab (heavy chain); Bobwhite quail lysozyme
UniProt: P00700
Pockets: 6 · best druggability 0.58

Structure

x-ray diffraction · 3 distinct chains · 15% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Hyhel-5 Fab (light chain)	protein	212	6% helix, 47% strand	—
H	Hyhel-5 Fab (heavy chain)	protein	214	7% helix, 49% strand	—
Y	Bobwhite quail lysozyme	protein	129	42% helix, 11% strand	P00700

Pockets

6 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	169	0.58	0.82	33	empty
2	242	0.47	0.74	44	empty
3	61	0.38	0.80	19	empty
4	103	0.37	0.75	21	empty
5	78	0.35	0.76	18	empty

Interfaces

3 interfaces between chains.

L–H · 1767 Å² buried · 15 hydrogen bonds · protein-protein
H–Y · 499 Å² buried · 7 hydrogen bonds · protein-protein
L–Y · 429 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

1BQL · Structure of an anti-hel Fab fragment complexed with bobwhite quail lysozyme · the same entry in another collection · chain L against L, TM-score 1.00
P00700 · AlphaFold monomer V2.0 prediction for lysozyme C (P00700) · a predicted model of the same protein · chain Y against A, TM-score 0.98

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 P00700
Elsewhere: RCSB PDB 1BQL · PDBe 1BQL · UniProt P00700

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