MolNFT v1 · #119342 · protein

Arabidopsis thaliana nuclear protein-only RNase P 2 (PRORP2)

5FT9 · Proteinaceous RNase P 2: “Arabidopsis thaliana nuclear protein-only RNase P 2 (PRORP2)”. X-ray diffraction, 1 ligand (ZN), 9 pockets (best druggability 0.60). MolNFT v1 #119342 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 5FT9
Type: protein
Length: 945 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Proteinaceous RNase P 2
EC: 3.1.26.5
UniProt: Q680B9
Ligands: ZN
Pockets: 9 · best druggability 0.60

Structure

x-ray diffraction · 2 distinct chains · 56% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Proteinaceous RNase P 2 (EC 3.1.26.5)	protein	472	56% helix, 10% strand	Q680B9
B	Proteinaceous RNase P 2 (EC 3.1.26.5)	protein	473	56% helix, 11% strand	Q680B9

Ligands and binding sites

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

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

Pockets

9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	369	0.60	0.77	36	empty
2	266	0.58	0.78	32	empty
3	307	0.57	0.76	40	empty
4	107	0.53	0.82	16	empty
5	217	0.51	0.77	35	empty

Interfaces

1 interface between chains.

A–B · 337 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

5FT9 · Arabidopsis thaliana nuclear protein-only RNase P 2 (PRORP2) · the same entry in another collection · chain A against A, TM-score 1.00
Q680B9 · AlphaFold monomer V2.0 prediction for proteinaceous RNase P 2 (Q680B9) · a predicted model of the same protein · chain A against A, TM-score 0.92

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 Q680B9
Elsewhere: RCSB PDB 5FT9 · PDBe 5FT9 · UniProt Q680B9

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