MolNFT v1 · #126919 · protein

Crystal structure of anti-T4 Fab fragment with T4

5MHE · Fab-fragment: “Crystal structure of anti-T4 Fab fragment with T4”. X-ray diffraction, 2 ligands (T44, SO4), 6 pockets (best druggability 0.63). MolNFT v1 #126919 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5MHE
Type: protein
Length: 432 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab-fragment
Ligands: T44, SO4
Pockets: 6 · best druggability 0.63

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Fab-fragment	protein	212	6% helix, 51% strand	—
H	Fab-fragment	protein	220	5% helix, 51% strand	—

Ligands and binding sites

T44 · 3,5,3',5'-tetraiodo-L-thyronine · ligand · chains L, H
SO4 · Sulfate ion · ion · chains L
GOL · Glycerol · additive · 2 copies · chains H, L

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

Pockets

6 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	130	0.63	0.86	21	T44
2	463	0.60	0.75	58	GOL
3	129	0.41	0.75	20	empty
4	117	0.40	0.75	24	empty
5	58	0.37	0.79	15	empty

Interfaces

1 interface between chains.

L–H · 1923 Å² buried · 19 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5MHE · Crystal structure of anti-T4 Fab fragment with T4 · the same entry in another collection · chain L against L, 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 5MHE · PDBe 5MHE

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