MolNFT v1 · #69133 · protein

Crystal structure of a cupin 2 conserved barrel domain protein from rhodopseudomonas palustris

3KGZ: “Crystal structure of a cupin 2 conserved barrel domain protein from rhodopseudomonas palustris”. X-ray diffraction, 1 ligand (MN), 3 pockets (best druggability 0.64). MolNFT v1 #69133 on GenesisL1: 3D structure, binding sites and…

PDB: 3KGZ
Type: protein
Length: 290 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cupin 2 conserved barrel domain protein
UniProt: B3QER1
Ligands: MN
Pockets: 3 · best druggability 0.64

Structure

x-ray diffraction · 1 distinct chain · 10% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Cupin 2 conserved barrel domain protein	protein	145	10% helix, 48% strand	B3QER1

Ligands and binding sites

MN · Manganese (II) ion · metal · 2 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	239	0.64	0.82	24	empty
2	193	0.61	0.82	25	empty
3	82	0.45	0.81	20	empty

Interfaces

1 interface between chains.

A–B · 1509 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

3KGZ · Crystal structure of a cupin 2 conserved barrel domain protein from Rhodopseudomonas… · 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 B3QER1
Elsewhere: RCSB PDB 3KGZ · PDBe 3KGZ · UniProt B3QER1

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