MolNFT v1 · #126168 · protein

Structures of dhbn domain of human blm helicase

5LUP · Blm protein: “Structures of dhbn domain of human blm helicase”. X-ray diffraction, 2 ligands (K, PO4), 6 pockets (best druggability 0.77). MolNFT v1 #126168 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5LUP
Type: protein
Length: 617 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Blm protein
UniProt: Q3B7X0
Ligands: K, PO4
Pockets: 6 · best druggability 0.77

Structure

x-ray diffraction · 8 distinct chains · 74% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, K, L	Blm protein	protein	50	76% helix, 0% strand	Q3B7X0
B	Blm protein	protein	51	76% helix, 0% strand	Q3B7X0
C	Blm protein	protein	54	70% helix, 0% strand	Q3B7X0
D, E	Blm protein	protein	53	70% helix, 0% strand	Q3B7X0
F, G	Blm protein	protein	52	73% helix, 0% strand	Q3B7X0
H	Blm protein	protein	52	81% helix, 0% strand	Q3B7X0
I	Blm protein	protein	51	73% helix, 0% strand	Q3B7X0
J	Blm protein	protein	49	73% helix, 0% strand	Q3B7X0

Ligands and binding sites

K · Potassium ion · metal · 2 copies · chains B, D
PO4 · Phosphate ion · ion · 2 copies · chains A, F, I, J

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

Pockets

6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1185	0.77	0.79	103	empty
2	264	0.56	0.77	41	empty
3	147	0.54	0.81	24	empty
4	273	0.54	0.75	37	empty
5	66	0.30	0.74	18	empty

Interfaces

26 interfaces between chains.

C–D · 1480 Å² buried · 4 hydrogen bonds · protein-protein
E–F · 1388 Å² buried · 4 hydrogen bonds · protein-protein
G–H · 1352 Å² buried · 4 hydrogen bonds · protein-protein
K–L · 1317 Å² buried · 1 hydrogen bond · protein-protein
I–J · 1306 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

5LUP · Structures of DHBN domain of human BLM helicase · the same entry in another collection · chain A against A, TM-score 1.00

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 Q3B7X0
Elsewhere: RCSB PDB 5LUP · PDBe 5LUP · UniProt Q3B7X0

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