MolNFT v1 · #156739 · protein + DNA

Mechanism of protease dependent dpc repair

6MDX · Sprt-like domain-containing protein spartan: “Mechanism of protease dependent dpc repair”. X-ray diffraction, 1 ligand (ZN), 3 pockets (best druggability 0.62). MolNFT v1 #156739 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 6MDX
Type: protein + DNA
Length: 185 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sprt-like domain-containing protein spartan; DNA (5'-D(P*CP*C)-3')
UniProt: Q9H040
Ligands: ZN
Pockets: 3 · best druggability 0.62

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Sprt-like domain-containing protein spartan	protein	183	38% helix, 17% strand	Q9H040
D	DNA (5'-D(PCPC)-3')	dna	2	—	—

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A
EDO · 1,2-ethanediol · additive · chains A
PGE · Triethylene glycol · additive · chains A
FLC · Citrate anion · additive · chains A

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	91	0.62	0.89	25	empty
2	352	0.60	0.77	42	EDO, ZN, FLC
3	70	0.41	0.80	19	empty

Interfaces

1 interface between chains.

A–D · 343 Å² buried · 9 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 5 modified (engineered, methylation).

Compared structures

6MDX · Mechanism of protease dependent DPC repair · the same entry in another collection · chain A against A, TM-score 1.00
Q9H040 · AlphaFold monomer V2.0 prediction for DNA-dependent metalloprotease sprtn (Q9H040) · a predicted model of the same protein · chain A against A, TM-score 0.75

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 Q9H040
Elsewhere: RCSB PDB 6MDX · PDBe 6MDX · UniProt Q9H040

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