MolNFT v1 · #63700 · protein

Crystal structure of APC1446, B.SUBTILIS yphp disulfide isomerase

3FHK · UPF0403 protein yphp: “Crystal structure of APC1446, B.SUBTILIS yphp disulfide isomerase”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.55). MolNFT v1 #63700 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 3FHK
Type: protein
Length: 584 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: UPF0403 protein yphp
UniProt: P54170
Ligands: SO4
Pockets: 4 · best druggability 0.55

Structure

x-ray diffraction · 2 distinct chains · 51% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E, F	UPF0403 protein yphp	protein	147	52% helix, 18% strand	P54170
D	UPF0403 protein yphp	protein	143	50% helix, 19% strand	P54170

Ligands and binding sites

SO4 · Sulfate ion · ion · 12 copies · chains A, D, E, F

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

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	274	0.55	0.76	40	empty
2	404	0.55	0.73	44	SO4
3	246	0.53	0.76	38	empty
4	100	0.37	0.74	20	empty

Interfaces

6 interfaces between chains.

D–E · 477 Å² buried · 4 hydrogen bonds · protein-protein
A–E · 441 Å² buried · 0 hydrogen bonds · protein-protein
D–F · 433 Å² buried · 2 hydrogen bonds · protein-protein
E–F · 381 Å² buried · 0 hydrogen bonds · protein-protein
A–D · 374 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3FHK · Crystal structure of APC1446, B.subtilis YphP disulfide isomerase · the same entry in another collection · chain F against F, TM-score 1.00
P54170 · AlphaFold monomer V2.0 prediction for UPF0403 protein yphp (P54170) · a predicted model of the same protein · chain D against A, TM-score 0.99

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P54170
Elsewhere: RCSB PDB 3FHK · PDBe 3FHK · UniProt P54170

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