MolNFT v1 · #184731 · protein

Naf-1 bound to M1 molecule

7P0P · Cdgsh iron-sulfur domain-containing protein 2: “Naf-1 bound to M1 molecule”. X-ray diffraction, 2 ligands (FES, 49I), 1 pocket (best druggability 0.69). MolNFT v1 #184731 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7P0P
Type: protein
Length: 262 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cdgsh iron-sulfur domain-containing protein 2
UniProt: Q8N5K1
Ligands: FES, 49I
Pockets: 1 · best druggability 0.69

Structure

x-ray diffraction · 3 distinct chains · 18% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Cdgsh iron-sulfur domain-containing protein 2	protein	65	18% helix, 28% strand	Q8N5K1
B	Cdgsh iron-sulfur domain-containing protein 2	protein	66	18% helix, 27% strand	Q8N5K1
D	Cdgsh iron-sulfur domain-containing protein 2	protein	66	17% helix, 26% strand	Q8N5K1

Ligands and binding sites

FES · Fe2/s2 (inorganic) cluster · ligand · 4 copies · chains A, B, C, D
49I · 2-benzamido-4-[(2~{R})-1,2,3,4-tetrahydronaphthalen-2-yl]thiophene-3-carboxylic acid · ligand · chains A, B, C, D

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	500	0.69	0.80	48	49I

Interfaces

6 interfaces between chains.

A–B · 1917 Å² buried · 50 hydrogen bonds · protein-protein
C–D · 1911 Å² buried · 52 hydrogen bonds · protein-protein
A–C · 199 Å² buried · 1 hydrogen bond · protein-protein
B–D · 143 Å² buried · 1 hydrogen bond · protein-protein
B–C · 87 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

7P0P · NAF-1 bound to M1 molecule · the same entry in another collection · chain D against D, TM-score 1.00
Q8N5K1 · AlphaFold monomer V2.0 prediction for cdgsh iron-sulfur domain- containing protein 2… · a predicted model of the same protein · chain A against A, TM-score 0.97

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 Q8N5K1
Elsewhere: RCSB PDB 7P0P · PDBe 7P0P · UniProt Q8N5K1

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