MolNFT v1 · #158540 · protein

Crystal structure of the rrm domain of S. pombe PUF1 in the P21 space group

6NX5 · Pumilio domain-containing protein C56F2.08C: “Crystal structure of the rrm domain of S. pombe PUF1 in the P21 space group”. X-ray diffraction, 2 pockets (best druggability 0.45). MolNFT v1 #158540 on GenesisL1: 3D structure, binding…

PDB: 6NX5
Type: protein
Length: 309 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pumilio domain-containing protein C56F2.08C
UniProt: O60059
Pockets: 2 · best druggability 0.45

Structure

x-ray diffraction · 4 distinct chains · 27% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pumilio domain-containing protein C56F2.08C	protein	83	23% helix, 30% strand	O60059
B	Pumilio domain-containing protein C56F2.08C	protein	77	29% helix, 35% strand	O60059
C	Pumilio domain-containing protein C56F2.08C	protein	74	30% helix, 30% strand	O60059
D	Pumilio domain-containing protein C56F2.08C	protein	75	27% helix, 32% strand	O60059

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 2 copies · chains B

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	132	0.45	0.77	28	empty
2	50	0.40	0.82	17	empty

Interfaces

5 interfaces between chains.

A–B · 986 Å² buried · 15 hydrogen bonds · protein-protein
C–D · 706 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 480 Å² buried · 13 hydrogen bonds · protein-protein
A–C · 262 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 231 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6NX5 · Crystal structure of the RRM domain of S. pombe Puf1 in the P21 space group · the same entry in another collection · chain D against D, TM-score 1.00
O60059 · AlphaFold monomer V2.0 prediction for pumilio domain-containing protein C56F2.08C (O60059) · a predicted model of the same protein · chain C 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 O60059
Elsewhere: RCSB PDB 6NX5 · PDBe 6NX5 · UniProt O60059

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