MolNFT v1 · #141039 · protein

Crystal structure of pml ring tetramer

5YUF · Protein pml: “Crystal structure of pml ring tetramer”. X-ray diffraction, 1 ligand (ZN), 1 pocket (best druggability 0.60). MolNFT v1 #141039 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5YUF
Type: protein
Length: 186 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein pml
UniProt: P29590
Ligands: ZN
Pockets: 1 · best druggability 0.60

Structure

x-ray diffraction · 3 distinct chains · 11% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Protein pml	protein	47	11% helix, 17% strand	P29590
C	Protein pml	protein	46	11% helix, 17% strand	P29590
D	Protein pml	protein	46	11% helix, 17% strand	P29590

Ligands and binding sites

ZN · Zinc ion · metal · 8 copies · chains A, B, C, D

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	461	0.60	0.75	41	empty

Interfaces

4 interfaces between chains.

C–D · 682 Å² buried · 2 hydrogen bonds · protein-protein
A–B · 680 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 331 Å² buried · 1 hydrogen bond · protein-protein
A–D · 330 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

5YUF · Crystal Structure of PML RING tetramer · the same entry in another collection · chain A against A, TM-score 1.00
P29590 · AlphaFold monomer V2.0 prediction for protein pml (P29590) · a predicted model of the same protein · chain A against A, TM-score 0.76

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 P29590
Elsewhere: RCSB PDB 5YUF · PDBe 5YUF · UniProt P29590

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