MolNFT v1 · #152472 · protein

Apo-form structure of the HRP3 pwwp domain

6IIP · Hepatoma-derived growth factor-related protein 3: “Apo-form structure of the HRP3 pwwp domain”. X-ray diffraction, 1 ligand (SO4), 3 pockets (best druggability 0.69). MolNFT v1 #152472 on GenesisL1: 3D structure, binding sites and…

PDB: 6IIP
Type: protein
Length: 175 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hepatoma-derived growth factor-related protein 3
UniProt: Q9Y3E1
Ligands: SO4
Pockets: 3 · best druggability 0.69

Structure

x-ray diffraction · 2 distinct chains · 26% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hepatoma-derived growth factor-related protein 3	protein	88	26% helix, 24% strand	Q9Y3E1
B	Hepatoma-derived growth factor-related protein 3	protein	87	26% helix, 24% strand	Q9Y3E1

Ligands and binding sites

SO4 · Sulfate ion · ion · 5 copies · chains A, B
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · 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	202	0.69	0.86	46	MES
2	146	0.47	0.77	27	empty
3	53	0.24	0.72	16	empty

Interfaces

1 interface between chains.

A–B · 647 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

6IIP · Apo-form structure of the HRP3 PWWP domain · the same entry in another collection · chain A against A, TM-score 1.00
Q9Y3E1 · AlphaFold monomer V2.0 prediction for hepatoma-derived growth factor- related protein 3… · a predicted model of the same protein · chain B against A, TM-score 0.93

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 Q9Y3E1
Elsewhere: RCSB PDB 6IIP · PDBe 6IIP · UniProt Q9Y3E1

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