MolNFT v1 · #11597 · protein

DNA protection and binding by E. COLI dps protein

1JRE · DNA protection during starvation protein: “DNA protection and binding by E. COLI dps protein”. X-ray diffraction, 1 ligand (CD), 20 pockets (best druggability 0.53). MolNFT v1 #11597 on GenesisL1: 3D structure, binding sites and…

PDB: 1JRE
Type: protein
Length: 1,871 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA protection during starvation protein
UniProt: P0ABT2
Ligands: CD
Pockets: 20 · best druggability 0.53

Structure

x-ray diffraction · 3 distinct chains · 73% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D, H	DNA protection during starvation protein	protein	157	72% helix, 1% strand	P0ABT2
C, G, J, K, L	DNA protection during starvation protein	protein	155	73% helix, 1% strand	P0ABT2
E, F, I	DNA protection during starvation protein	protein	156	73% helix, 1% strand	P0ABT2

Ligands and binding sites

CD · Cadmium ion · metal · 13 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 12 copies · chains A, E, I, H, J, B, K, L, C, G, F, D

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

Pockets

20 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	220	0.53	0.77	20	empty
2	221	0.53	0.78	25	empty
3	226	0.52	0.77	23	empty
4	222	0.52	0.77	21	empty
5	192	0.48	0.76	37	CD, TRS

Interfaces

30 interfaces between chains.

K–L · 1616 Å² buried · 18 hydrogen bonds · protein-protein
C–D · 1613 Å² buried · 14 hydrogen bonds · protein-protein
I–J · 1605 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 1601 Å² buried · 15 hydrogen bonds · protein-protein
E–F · 1599 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

1JRE · DNA protection and binding by E. COLI dps protein · 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 1JRE · PDBe 1JRE · UniProt P0ABT2

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