MolNFT v1 · #171965 · protein

Crystal structure of human NDRG1

6ZMM · Protein NDRG1: “Crystal structure of human NDRG1”. X-ray diffraction, 1 ligand (CL), 7 pockets (best druggability 0.46). MolNFT v1 #171965 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6ZMM
Type: protein
Length: 503 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein NDRG1
UniProt: Q92597
Ligands: CL
Pockets: 7 · best druggability 0.46

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein NDRG1	protein	251	41% helix, 20% strand	Q92597
B	Protein NDRG1	protein	252	43% helix, 20% strand	Q92597

Ligands and binding sites

CL · Chloride ion · ion · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	141	0.46	0.77	22	empty
2	65	0.41	0.81	20	empty
3	113	0.41	0.76	24	empty
4	123	0.41	0.75	15	empty
5	61	0.39	0.80	20	empty

Interfaces

1 interface between chains.

A–B · 930 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

6ZMM · Crystal structure of human NDRG1 · the same entry in another collection · chain A against A, TM-score 1.00
Q92597 · AlphaFold monomer V2.0 prediction for protein NDRG1 (Q92597) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 Q92597
Elsewhere: RCSB PDB 6ZMM · PDBe 6ZMM · UniProt Q92597

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