MolNFT v1 · #127015 · protein

Structures of dhbn domain of human blm helicase

5MK5 · Bloom syndrome protein: “Structures of dhbn domain of human blm helicase”. X-ray diffraction, 2 ligands (K, IOD), 2 pockets (best druggability 0.39). MolNFT v1 #127015 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5MK5
Type: protein
Length: 203 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bloom syndrome protein
EC: 3.6.4.12
UniProt: P54132
Ligands: K, IOD
Pockets: 2 · best druggability 0.39

Structure

x-ray diffraction · 3 distinct chains · 78% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Bloom syndrome protein (EC 3.6.4.12)	protein	51	76% helix, 0% strand	P54132
B, C	Bloom syndrome protein (EC 3.6.4.12)	protein	52	79% helix, 0% strand	P54132
D	Bloom syndrome protein (EC 3.6.4.12)	protein	48	79% helix, 0% strand	P54132

Ligands and binding sites

K · Potassium ion · metal · 3 copies · chains A, C
IOD · Iodide ion · ion · 20 copies · chains A, B, C, D

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

Pockets

2 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	108	0.39	0.75	22	IOD
2	61	0.28	0.72	13	IOD

Interfaces

5 interfaces between chains.

A–B · 1330 Å² buried · 2 hydrogen bonds · protein-protein
C–D · 1299 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 189 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 148 Å² buried · 1 hydrogen bond · protein-protein
B–C · 134 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5MK5 · Structures of DHBN domain of human BLM helicase · the same entry in another collection · chain D against D, TM-score 1.00
P54132 · AlphaFold monomer V2.0 prediction for bloom syndrome protein (P54132) · a predicted model of the same protein · chain D against A, TM-score 0.88

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 P54132
Elsewhere: RCSB PDB 5MK5 · PDBe 5MK5 · UniProt P54132

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.