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Crystal structure of 2H4 Fab

Analyse Crystal structure of 2H4 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5YWF
Type: protein
Length: 866 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 2H4 light chain; 2H4 heavy chain
Pockets: 12 · best druggability 0.64

Structure

x-ray diffraction · 2 distinct chains · 8% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	2H4 light chain	protein	215	5% helix, 50% strand	—
B, D	2H4 heavy chain	protein	218	11% helix, 51% strand	—

Pockets

12 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	507	0.64	0.77	55	empty
2	71	0.53	0.86	20	empty
3	136	0.46	0.78	26	empty
4	196	0.45	0.74	30	empty
5	154	0.44	0.75	30	empty

Interfaces

5 interfaces between chains.

A–B · 1962 Å² buried · 18 hydrogen bonds · protein-protein
C–D · 1891 Å² buried · 19 hydrogen bonds · protein-protein
A–C · 287 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 214 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 212 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 disulfide (disulfide).

Compared structures

5YWF · Crystal structure of 2H4 Fab · the same entry in another collection · chain A against A, 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 5YWF · PDBe 5YWF

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