MolNFT v1 · #140358 · protein

Periplasmic heme-binding protein rhut from roseiflexus sp. rs-1 in apo form

5Y8B · Periplasmic binding protein: “Periplasmic heme-binding protein rhut from roseiflexus sp. rs-1 in apo form”. X-ray diffraction, 1 ligand (MG), 1 pocket (best druggability 0.66). MolNFT v1 #140358 on GenesisL1: 3D structure, binding…

PDB: 5Y8B
Type: protein
Length: 263 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Periplasmic binding protein
UniProt: A5UZ69
Ligands: MG
Pockets: 1 · best druggability 0.66

Structure

x-ray diffraction · 1 distinct chain · 46% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Periplasmic binding protein	protein	263	46% helix, 17% strand	A5UZ69

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains A

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	462	0.66	0.78	40	MG

Compared structures

5Y8B · Periplasmic heme-binding protein RhuT from Roseiflexus sp. RS-1 in apo form · 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 A5UZ69
Elsewhere: RCSB PDB 5Y8B · PDBe 5Y8B · UniProt A5UZ69

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