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Crystal structure of regnase pin domain, form I

Analyse Crystal structure of regnase pin domain, form I in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5H9V
Type: protein
Length: 643 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribonuclease ZC3H12A
EC: 3.1.-.-
UniProt: Q5D1E7
Ligands: NA
Pockets: 6 · best druggability 0.61

Structure

x-ray diffraction · 3 distinct chains · 39% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ribonuclease ZC3H12A (EC 3.1.-.-)	protein	161	39% helix, 22% strand	Q5D1E7
B	Ribonuclease ZC3H12A (EC 3.1.-.-)	protein	158	40% helix, 25% strand	Q5D1E7
C, D	Ribonuclease ZC3H12A (EC 3.1.-.-)	protein	162	38% helix, 24% strand	Q5D1E7

Ligands and binding sites

NA · Sodium ion · metal · 4 copies · chains A, B, C, D

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

Pockets

6 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	282	0.61	0.79	42	empty
2	308	0.60	0.78	45	empty
3	236	0.49	0.74	33	empty
4	187	0.47	0.75	24	empty
5	66	0.27	0.72	14	empty

Interfaces

3 interfaces between chains.

C–D · 951 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 896 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 422 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 modified (engineered).

Compared structures

5H9V · Crystal structure of Regnase PIN domain, form I · the same entry in another collection · chain A against A, TM-score 1.00
Q5D1E7 · AlphaFold monomer V2.0 prediction for endoribonuclease ZC3H12A (Q5D1E7) · a predicted model of the same protein · chain C 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 Q5D1E7
Elsewhere: RCSB PDB 5H9V · PDBe 5H9V · UniProt Q5D1E7

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