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DNA protection and binding by E. COLI dps protein

Analyse DNA protection and binding by E. COLI dps protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1JTS
Type: protein
Length: 3,727 residues
Chains: 24
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA protection during starvation protein
UniProt: P0ABT2
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 5 distinct chains · 73% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, F, G, L, V	DNA protection during starvation protein	protein	155	74% helix, 1% strand	P0ABT2
C, D, H, I, K, P, Q	DNA protection during starvation protein	protein	154	74% helix, 1% strand	P0ABT2
E, M, N, O, R, S, T, W, X	DNA protection during starvation protein	protein	156	74% helix, 1% strand	P0ABT2
J	DNA protection during starvation protein	protein	158	70% helix, 1% strand	P0ABT2
U	DNA protection during starvation protein	protein	157	73% helix, 1% strand	P0ABT2

Ligands and binding sites

TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 24 copies · chains A, E, I, H, J, C, F, L, D, G, B, K, M, Q, U, T, V, P, R, S, N, X, O, W

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	123	0.80	0.97	19	empty
2	111	0.79	0.98	18	empty
3	111	0.79	0.97	20	empty
4	112	0.78	0.97	19	empty
5	103	0.78	0.98	20	empty

Interfaces

62 interfaces between chains.

K–L · 1572 Å² buried · 15 hydrogen bonds · protein-protein
U–V · 1571 Å² buried · 17 hydrogen bonds · protein-protein
S–T · 1570 Å² buried · 17 hydrogen bonds · protein-protein
E–F · 1568 Å² buried · 17 hydrogen bonds · protein-protein
W–X · 1566 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

1JTS · DNA protection and binding by E. COLI dps protein · the same entry in another collection · chain G against G, 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 1JTS · PDBe 1JTS · UniProt P0ABT2

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