MolNFT v1 · #33153 · protein

Crystal structure of zipd from escherichia COLI

2CBN · Ribonuclease Z: “Crystal structure of zipd from escherichia COLI”. X-ray diffraction, 1 ligand (ZN), 2 pockets (best druggability 0.39). MolNFT v1 #33153 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2CBN
Type: protein
Length: 306 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribonuclease Z
EC: 3.1.26.11
UniProt: P0A8V0
Ligands: ZN
Pockets: 2 · best druggability 0.39

Structure

x-ray diffraction · 1 distinct chain · 28% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ribonuclease Z (EC 3.1.26.11)	protein	306	28% helix, 27% strand	P0A8V0

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	58	0.39	0.80	12	empty
2	53	0.28	0.75	17	empty

Compared structures

2CBN · Crystal structure of ZipD from Escherichia coli · the same entry in another collection · chain A against A, TM-score 1.00
P0A8V0 · AlphaFold monomer V2.0 prediction for ribonuclease bn (P0A8V0) · a predicted model of the same protein · chain A against A, TM-score 0.94

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 P0A8V0
Elsewhere: RCSB PDB 2CBN · PDBe 2CBN · UniProt P0A8V0

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