MolNFT v1 · #88284 · protein

Crystal structure of the neuronal isoform of ptb

4CQ1 · Polypyrimidine tract-binding protein 2: “Crystal structure of the neuronal isoform of ptb”. X-ray diffraction, 2 ligands (ZN, CL), 16 pockets (best druggability 0.74). MolNFT v1 #88284 on GenesisL1: 3D structure, binding sites and…

PDB: 4CQ1
Type: protein
Length: 1,522 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Polypyrimidine tract-binding protein 2
UniProt: Q9UKA9
Ligands: ZN, CL
Pockets: 16 · best druggability 0.74

Structure

x-ray diffraction · 4 distinct chains · 22% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, F, G, H	Polypyrimidine tract-binding protein 2	protein	191	22% helix, 30% strand	Q9UKA9
B	Polypyrimidine tract-binding protein 2	protein	192	22% helix, 27% strand	Q9UKA9
C	Polypyrimidine tract-binding protein 2	protein	188	23% helix, 28% strand	Q9UKA9
D, E	Polypyrimidine tract-binding protein 2	protein	189	22% helix, 29% strand	Q9UKA9

Ligands and binding sites

ZN · Zinc ion · metal · 12 copies · chains A, C, D, B, E, G, H, F
CL · Chloride ion · ion · 8 copies · chains A, C, B, D, E, G, F, H

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

Pockets

16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	893	0.74	0.78	85	empty
2	1029	0.72	0.76	111	empty
3	699	0.72	0.78	78	ZN, CL
4	703	0.68	0.76	67	empty
5	362	0.64	0.79	46	empty

Interfaces

14 interfaces between chains.

A–F · 550 Å² buried · 8 hydrogen bonds · protein-protein
C–H · 473 Å² buried · 3 hydrogen bonds · protein-protein
B–E · 450 Å² buried · 4 hydrogen bonds · protein-protein
D–G · 400 Å² buried · 2 hydrogen bonds · protein-protein
F–H · 394 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

4CQ1 · Crystal structure of the neuronal isoform of PTB · the same entry in another collection · chain H against H, TM-score 1.00
Q9UKA9 · AlphaFold monomer V2.0 prediction for polypyrimidine tract-binding protein 2 (Q9UKA9) · a predicted model of the same protein · chain C against A, TM-score 0.99

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 Q9UKA9
Elsewhere: RCSB PDB 4CQ1 · PDBe 4CQ1 · UniProt Q9UKA9

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