MolNFT v1 · #138146 · protein + DNA

Zinc finger region of MBD1 in complex with cpg DNA

5W9Q · Methyl-cpg-binding domain protein 1: “Zinc finger region of MBD1 in complex with cpg DNA”. X-ray diffraction, 2 ligands (ZN, UNX), 4 pockets (best druggability 0.41). MolNFT v1 #138146 on GenesisL1: 3D structure, binding sites and…

PDB: 5W9Q
Type: protein + DNA
Length: 158 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Methyl-cpg-binding domain protein 1; DNA
UniProt: Q9UIS9
Ligands: ZN, UNX
Pockets: 4 · best druggability 0.41

Structure

x-ray diffraction · 3 distinct chains · 33% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Methyl-cpg-binding domain protein 1	protein	56	32% helix, 0% strand	Q9UIS9
B	Methyl-cpg-binding domain protein 1	protein	54	33% helix, 0% strand	Q9UIS9
C, D, E, F	DNA	dna	12	—	—

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, B
UNX · Unknown atom or ion · ion · 16 copies · chains A, C, D, B, F, E

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

Pockets

4 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	70	0.41	0.80	17	UNX
2	90	0.40	0.77	14	empty
3	106	0.36	0.74	14	UNX
4	114	0.34	0.73	16	UNX

Interfaces

7 interfaces between chains.

C–D · 547 Å² buried · 49 hydrogen bonds · nucleic-nucleic
E–F · 545 Å² buried · 47 hydrogen bonds · nucleic-nucleic
A–C · 493 Å² buried · 6 hydrogen bonds · protein-nucleic
B–E · 422 Å² buried · 7 hydrogen bonds · protein-nucleic
A–D · 404 Å² buried · 8 hydrogen bonds · protein-nucleic

Compared structures

5W9Q · Zinc finger region of MBD1 in complex with CpG DNA · the same entry in another collection · chain F against F, TM-score 1.00
Q9UIS9 · AlphaFold monomer V2.0 prediction for methyl-cpg-binding domain protein 1 (Q9UIS9) · 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 Q9UIS9
Elsewhere: RCSB PDB 5W9Q · PDBe 5W9Q · UniProt Q9UIS9

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