MolNFT v1 · #127456 · protein

Structure of DC8E8 Fab crystallized at pH 8.5

5MX3 · Antibody Fab heavy chain: “Structure of DC8E8 Fab crystallized at pH 8.5”. X-ray diffraction, 10 pockets (best druggability 0.72). MolNFT v1 #127456 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5MX3
Type: protein
Length: 876 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Antibody Fab heavy chain; Antibody kappa chain
Pockets: 10 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H, A	Antibody Fab heavy chain	protein	220	8% helix, 50% strand	—
L, B	Antibody kappa chain	protein	218	5% helix, 54% strand	—

Pockets

10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1036	0.72	0.76	105	empty
2	751	0.67	0.75	64	empty
3	755	0.67	0.75	66	empty
4	187	0.54	0.79	28	empty
5	171	0.51	0.78	29	empty

Interfaces

5 interfaces between chains.

H–L · 1865 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 1839 Å² buried · 18 hydrogen bonds · protein-protein
H–A · 272 Å² buried · 9 hydrogen bonds · protein-protein
H–B · 98 Å² buried · 0 hydrogen bonds · protein-protein
L–A · 67 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 2 modified (disulfide, cyclization).

Compared structures

5MX3 · Structure of DC8E8 Fab crystallized at pH 8.5 · 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 5MX3 · PDBe 5MX3

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