MolNFT v1 · #4495 · protein

The crystal structure of dps, a ferritin homolog that binds and protects DNA

1DPS: “The crystal structure of dps, a ferritin homolog that binds and protects DNA”. X-ray diffraction, 1 ligand (NA), 20 pockets (best druggability 0.76). MolNFT v1 #4495 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1DPS
Type: protein
Length: 1,855 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dps
UniProt: P0ABT2
Ligands: NA
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 3 distinct chains · 72% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dps	protein	159	71% helix, 1% strand	P0ABT2
B, C, E, F, G, H, I, J, K, L	Dps	protein	154	74% helix, 1% strand	P0ABT2
D	Dps	protein	156	72% helix, 1% strand	P0ABT2

Ligands and binding sites

NA · Sodium ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L

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

Pockets

20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	81	0.76	0.98	20	empty
2	85	0.76	0.97	21	empty
3	73	0.75	0.98	21	empty
4	82	0.75	0.97	20	empty
5	71	0.75	0.98	21	empty

Interfaces

30 interfaces between chains.

E–G · 1611 Å² buried · 19 hydrogen bonds · protein-protein
J–L · 1609 Å² buried · 19 hydrogen bonds · protein-protein
F–H · 1608 Å² buried · 18 hydrogen bonds · protein-protein
I–K · 1606 Å² buried · 19 hydrogen bonds · protein-protein
B–D · 1606 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

1DPS · The crystal structure of dps, a ferritin homolog that binds and protects DNA · the same entry in another collection · chain L against L, 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 P0ABT2
Elsewhere: RCSB PDB 1DPS · PDBe 1DPS · UniProt P0ABT2

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