MolNFT v1 · #16442 · protein

RNase P protein from thermotoga maritima

1NZ0 · Ribonuclease P protein component: “RNase P protein from thermotoga maritima”. X-ray diffraction, 1 ligand (SO4), 3 pockets (best druggability 0.63). MolNFT v1 #16442 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1NZ0
Type: protein
Length: 437 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribonuclease P protein component
EC: 3.1.26.5
UniProt: Q9X1H4
Ligands: SO4
Pockets: 3 · best druggability 0.63

Structure

x-ray diffraction · 4 distinct chains · 47% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ribonuclease P protein component (EC 3.1.26.5)	protein	109	49% helix, 20% strand	Q9X1H4
C	Ribonuclease P protein component (EC 3.1.26.5)	protein	107	48% helix, 21% strand	Q9X1H4
B	Ribonuclease P protein component (EC 3.1.26.5)	protein	110	47% helix, 20% strand	Q9X1H4
D	Ribonuclease P protein component (EC 3.1.26.5)	protein	111	46% helix, 20% strand	Q9X1H4

Ligands and binding sites

SO4 · Sulfate ion · ion · 16 copies · chains A, C, B, D

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	377	0.63	0.78	40	SO4
2	347	0.60	0.77	37	SO4
3	51	0.28	0.74	14	empty

Interfaces

4 interfaces between chains.

A–C · 707 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 665 Å² buried · 4 hydrogen bonds · protein-protein
C–D · 37 Å² buried · 1 hydrogen bond · protein-protein
A–D · 15 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (engineered).

Compared structures

1NZ0 · RNase P protein from thermotoga maritima · the same entry in another collection · chain D against D, TM-score 1.00
Q9X1H4 · AlphaFold monomer V2.0 prediction for ribonuclease P protein component (Q9X1H4) · a predicted model of the same protein · chain C against A, TM-score 0.97

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 Q9X1H4
Elsewhere: RCSB PDB 1NZ0 · PDBe 1NZ0 · UniProt Q9X1H4

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