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Structure of holo form of a periplasmic heme binding protein

Analyse Structure of holo form of a periplasmic heme binding protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3NU1
Type: protein
Length: 508 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hemin-binding periplasmic protein
UniProt: Q1C0R0
Ligands: HEM
Pockets: 3 · best druggability 0.66

Structure

x-ray diffraction · 1 distinct chain · 44% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Hemin-binding periplasmic protein	protein	254	44% helix, 17% strand	Q1C0R0

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B

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

Pockets

3 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	625	0.66	0.76	70	HEM
2	221	0.52	0.76	29	HEM
3	66	0.32	0.75	17	empty

Interfaces

1 interface between chains.

A–B · 458 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

3NU1 · Structure of holo form of a periplasmic heme binding protein · 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 Q1C0R0
Elsewhere: RCSB PDB 3NU1 · PDBe 3NU1 · UniProt Q1C0R0

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