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Crystal form I of yfib belonging to space groups P21

Analyse Crystal form I of yfib belonging to space groups P21 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5EAZ
Type: protein
Length: 540 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Yfib
UniProt: Q9I4L6
Ligands: SO4
Pockets: 8 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 45% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Yfib	protein	135	45% helix, 20% strand	Q9I4L6

Ligands and binding sites

SO4 · Sulfate ion · ion · chains A

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

Pockets

8 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	456	0.72	0.82	49	empty
2	377	0.64	0.79	35	empty
3	168	0.61	0.83	34	empty
4	128	0.41	0.75	21	empty
5	135	0.41	0.75	22	empty

Interfaces

5 interfaces between chains.

B–C · 1174 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 345 Å² buried · 1 hydrogen bond · protein-protein
C–D · 323 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 282 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 207 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

5EAZ · crystal form I of YfiB belonging to space groups P21 · 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
Every structure of UniProt Q9I4L6
Elsewhere: RCSB PDB 5EAZ · PDBe 5EAZ · UniProt Q9I4L6

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