MolNFT v2 · #153578 · protein

Crystal structure of PML B1-box multimers

6IMQ · Protein PML: “Crystal structure of PML B1-box multimers”. X-ray diffraction at 2.06, 2 ligands (ZN, CL), 3 pockets (best druggability 0.77). MolNFT v2 #153578 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6IMQ
Type: protein
Length: 197 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.06
Source: Homo sapiens
Molecule: Protein PML
UniProt: P29590
Ligands: ZN, CL
Pockets: 3 · best druggability 0.77

Structure

x-ray diffraction · resolution 2.06 · 2 distinct chains · 20% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D	Protein PML	protein	49	20% helix, 31% strand	P29590
B	Protein PML	protein	50	20% helix, 30% strand	P29590

Ligands and binding sites

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

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	685	0.77	0.82	45	CL
2	93	0.37	0.75	14	empty
3	70	0.33	0.75	14	empty

Interfaces

5 interfaces between chains.

C–D · 954 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 949 Å² buried · 19 hydrogen bonds · protein-protein
A–C · 237 Å² buried · 1 hydrogen bond · protein-protein
B–C · 128 Å² buried · 1 hydrogen bond · protein-protein
A–D · 105 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6IMQ · Crystal structure of pml B1-box multimers · 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 B against A, TM-score 0.88

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 6IMQ · PDBe 6IMQ · UniProt P29590

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