MolNFT v1 · #126921 · protein

Crystal structure of anti-T4 Fab fragment with tetraiodobpa

5MHG · Fab-fragment: “Crystal structure of anti-T4 Fab fragment with tetraiodobpa”. X-ray diffraction, 2 ligands (4IB, SO4), 6 pockets (best druggability 0.64). MolNFT v1 #126921 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5MHG
Type: protein
Length: 433 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab-fragment
Ligands: 4IB, SO4
Pockets: 6 · best druggability 0.64

Structure

x-ray diffraction · 2 distinct chains · 4% helix, 53% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Fab-fragment	protein	213	6% helix, 55% strand	—
H	Fab-fragment	protein	220	3% helix, 50% strand	—

Ligands and binding sites

4IB · Tetraiodobisphenola · ligand · chains L, H
SO4 · Sulfate ion · ion · chains 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	165	0.64	0.85	21	4IB
2	392	0.57	0.75	45	empty
3	127	0.42	0.75	23	empty
4	120	0.40	0.75	22	empty
5	82	0.37	0.77	18	empty

Interfaces

1 interface between chains.

L–H · 1974 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5MHG · Crystal structure of anti-T4 Fab fragment with tetraiodoBPA · 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 5MHG · PDBe 5MHG

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