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Structure of porphyromonas gingivalis heme-binding protein hmuy in complex with heme

Analyse Structure of porphyromonas gingivalis heme-binding protein hmuy in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3H8T
Type: protein
Length: 364 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hmuy
UniProt: A2I2W2
Ligands: HEM, SO4
Pockets: 2 · best druggability 0.69

Structure

x-ray diffraction · 1 distinct chain · 7% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Hmuy	protein	182	7% helix, 52% strand	A2I2W2

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 4 copies · chains A, B
GOL · Glycerol · additive · 6 copies · chains A, B

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

Pockets

2 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	211	0.69	0.86	24	HEM, GOL
2	222	0.68	0.85	25	HEM, GOL

Interfaces

1 interface between chains.

A–B · 107 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3H8T · Structure of Porphyromonas gingivalis heme-binding protein HmuY in complex with Heme · 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 A2I2W2
Elsewhere: RCSB PDB 3H8T · PDBe 3H8T · UniProt A2I2W2

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