MolNFT v1 · #127347 · protein

Crystal structure of a long form RNase Z from yeast

5MTZ · Ribonuclease Z: “Crystal structure of a long form RNase Z from yeast”. X-ray diffraction, 2 ligands (ZN, PO4), 18 pockets (best druggability 0.76). MolNFT v1 #127347 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5MTZ
Type: protein
Length: 1,523 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribonuclease Z
EC: 3.1.26.11
UniProt: P36159
Ligands: ZN, PO4
Pockets: 18 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 29% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ribonuclease Z (EC 3.1.26.11)	protein	768	31% helix, 24% strand	P36159
B	Ribonuclease Z (EC 3.1.26.11)	protein	755	27% helix, 25% strand	P36159

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, B
PO4 · Phosphate ion · ion · 2 copies · chains A, B

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

Pockets

18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1092	0.76	0.78	94	PO4
2	644	0.73	0.80	63	empty
3	67	0.73	0.98	17	empty
4	66	0.73	0.98	19	empty
5	569	0.72	0.80	67	empty

Interfaces

1 interface between chains.

A–B · 900 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 36 modified (engineered).

Compared structures

5MTZ · Crystal structure of a long form RNase Z from yeast · the same entry in another collection · chain A against A, TM-score 1.00
P36159 · AlphaFold monomer V2.0 prediction for ribonuclease Z (P36159) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 P36159
Elsewhere: RCSB PDB 5MTZ · PDBe 5MTZ · UniProt P36159

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