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Crystal structure of SFH5

Analyse Crystal structure of SFH5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6W32
Type: protein
Length: 852 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phosphatidylinositol transfer protein SFH5
UniProt: A6ZQI5
Ligands: HEM
Pockets: 15 · best druggability 0.85

Structure

x-ray diffraction · 3 distinct chains · 43% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Phosphatidylinositol transfer protein SFH5	protein	288	49% helix, 11% strand	A6ZQI5
A	Phosphatidylinositol transfer protein SFH5	protein	278	42% helix, 12% strand	A6ZQI5
C	Phosphatidylinositol transfer protein SFH5	protein	286	39% helix, 8% strand	A6ZQI5

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 3 copies · chains B, A, C

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

Pockets

15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	406	0.85	0.92	48	HEM
2	387	0.84	0.92	53	HEM
3	465	0.82	0.89	55	HEM
4	102	0.76	0.96	27	empty
5	86	0.73	0.96	26	empty

Interfaces

2 interfaces between chains.

B–A · 942 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 475 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6W32 · Crystal structure of Sfh5 · the same entry in another collection · chain B against B, TM-score 1.00
A6ZQI5 · AlphaFold monomer V2.0 prediction for phosphatidylinositol transfer protein SFH5 (A6ZQI5) · a predicted model of the same protein · chain B against A, TM-score 0.97

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 A6ZQI5
Elsewhere: RCSB PDB 6W32 · PDBe 6W32 · UniProt A6ZQI5

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