MolNFT v1 · #140979 · protein

Crystal structure of antibody 1H1 Fab

5YSL · 1H1 heavy chain: “Crystal structure of antibody 1H1 Fab”. X-ray diffraction, 17 pockets (best druggability 0.75). MolNFT v1 #140979 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5YSL
Type: protein
Length: 1,693 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 1H1 heavy chain; 1H1 light chain
Pockets: 17 · best druggability 0.75

Structure

x-ray diffraction · 3 distinct chains · 8% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	1H1 heavy chain	protein	211	7% helix, 51% strand	—
B, D, F, H	1H1 light chain	protein	213	7% helix, 53% strand	—
C, E, G	1H1 heavy chain	protein	210	9% helix, 49% strand	—

Pockets

17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	888	0.75	0.79	112	empty
2	767	0.74	0.80	57	empty
3	522	0.70	0.80	69	empty
4	391	0.68	0.81	42	empty
5	829	0.68	0.75	84	empty

Interfaces

17 interfaces between chains.

A–B · 1737 Å² buried · 18 hydrogen bonds · protein-protein
G–H · 1730 Å² buried · 19 hydrogen bonds · protein-protein
C–D · 1728 Å² buried · 19 hydrogen bonds · protein-protein
E–F · 1693 Å² buried · 22 hydrogen bonds · protein-protein
C–E · 427 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

5YSL · Crystal structure of antibody 1H1 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 5YSL · PDBe 5YSL

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