MolNFT v1 · #104068 · protein

Crystal structure of PHC3 SAM L967R

4PZO · Polyhomeotic-like protein 3: “Crystal structure of PHC3 SAM L967R”. X-ray diffraction, 1 pocket (best druggability 0.36). MolNFT v1 #104068 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4PZO
Type: protein
Length: 426 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Polyhomeotic-like protein 3
UniProt: Q8NDX5
Pockets: 1 · best druggability 0.36

Structure

x-ray diffraction · 5 distinct chains · 65% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Polyhomeotic-like protein 3	protein	71	65% helix, 0% strand	Q8NDX5
B, F	Polyhomeotic-like protein 3	protein	71	66% helix, 0% strand	Q8NDX5
C	Polyhomeotic-like protein 3	protein	71	65% helix, 0% strand	Q8NDX5
D	Polyhomeotic-like protein 3	protein	70	66% helix, 0% strand	Q8NDX5
E	Polyhomeotic-like protein 3	protein	72	63% helix, 0% strand	Q8NDX5

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	53	0.36	0.79	12	empty

Interfaces

5 interfaces between chains.

E–F · 546 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 531 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 526 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 522 Å² buried · 5 hydrogen bonds · protein-protein
D–E · 508 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 modified (artifact).

Compared structures

4PZO · Crystal structure of PHC3 SAM L967R · the same entry in another collection · chain F against F, TM-score 1.00
Q8NDX5 · AlphaFold monomer V2.0 prediction for polyhomeotic-like protein 3 (Q8NDX5) · a predicted model of the same protein · chain D 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 Q8NDX5
Elsewhere: RCSB PDB 4PZO · PDBe 4PZO · UniProt Q8NDX5

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