MolNFT v1 · #105436 · protein

Structure of pngf-II in P21 space group

4R4Z: “Structure of pngf-II in P21 space group”. X-ray diffraction, 20 pockets (best druggability 0.81). MolNFT v1 #105436 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4R4Z
Type: protein
Length: 2,154 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pngf-II
EC: 2.7.7.7
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 3 distinct chains · 11% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pngf-II (EC 2.7.7.7)	protein	538	11% helix, 43% strand	—
B, C	Pngf-II (EC 2.7.7.7)	protein	539	11% helix, 43% strand	—
D	Pngf-II (EC 2.7.7.7)	protein	538	11% helix, 44% strand	—

Pockets

20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	242	0.81	0.94	30	empty
2	237	0.81	0.94	29	empty
3	939	0.74	0.77	93	empty
4	720	0.73	0.79	95	empty
5	647	0.70	0.78	83	empty

Interfaces

4 interfaces between chains.

A–B · 2668 Å² buried · 35 hydrogen bonds · protein-protein
C–D · 2565 Å² buried · 34 hydrogen bonds · protein-protein
B–C · 333 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 25 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

4R4Z · Structure of PNGF-II in P21 space group · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 4R4Z · PDBe 4R4Z

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