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Crystal structure of human NDRG3 C30S mutant

Analyse Crystal structure of human NDRG3 C30S mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6L4H
Type: protein
Length: 1,117 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein NDRG3
UniProt: Q9UGV2
Pockets: 16 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein NDRG3	protein	289	38% helix, 17% strand	Q9UGV2
B, C, D	Protein NDRG3	protein	276	41% helix, 20% strand	Q9UGV2

Pockets

16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	225	0.81	0.94	33	empty
2	228	0.80	0.94	33	empty
3	795	0.77	0.81	77	empty
4	463	0.70	0.81	58	empty
5	416	0.62	0.77	54	empty

Interfaces

5 interfaces between chains.

A–B · 852 Å² buried · 5 hydrogen bonds · protein-protein
C–D · 744 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 527 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 379 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 27 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6L4H · Crystal structure of human NDRG3 C30S mutant · the same entry in another collection · chain A against A, TM-score 1.00
Q9UGV2 · AlphaFold monomer V2.0 prediction for protein NDRG3 (Q9UGV2) · a predicted model of the same protein · chain B 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 Q9UGV2
Elsewhere: RCSB PDB 6L4H · PDBe 6L4H · UniProt Q9UGV2

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