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Crystal structure of C-terminal deletion mutant of mycobacterium smegmatis dps

Analyse Crystal structure of C-terminal deletion mutant of mycobacterium smegmatis dps in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2YW7
Type: protein
Length: 1,455 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Starvation-induced DNA protecting protein
UniProt: A0R692
Pockets: 20 · best druggability 0.73

Structure

x-ray diffraction · 6 distinct chains · 72% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, F	Starvation-induced DNA protecting protein	protein	146	73% helix, 3% strand	A0R692
B, D, E	Starvation-induced DNA protecting protein	protein	145	70% helix, 1% strand	A0R692
C	Starvation-induced DNA protecting protein	protein	147	74% helix, 3% strand	A0R692
G	Starvation-induced DNA protecting protein	protein	144	74% helix, 3% strand	A0R692
H, J	Starvation-induced DNA protecting protein	protein	146	70% helix, 1% strand	A0R692
I	Starvation-induced DNA protecting protein	protein	145	70% helix, 1% strand	A0R692

Pockets

20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	88	0.73	0.96	15	empty
2	78	0.71	0.95	15	empty
3	503	0.67	0.78	50	empty
4	299	0.54	0.75	35	empty
5	212	0.53	0.77	28	empty

Interfaces

18 interfaces between chains.

A–E · 1364 Å² buried · 23 hydrogen bonds · protein-protein
B–G · 1353 Å² buried · 19 hydrogen bonds · protein-protein
H–J · 1346 Å² buried · 19 hydrogen bonds · protein-protein
D–I · 1342 Å² buried · 21 hydrogen bonds · protein-protein
C–F · 1313 Å² buried · 23 hydrogen bonds · protein-protein

Compared structures

2YW7 · Crystal structure of C-terminal deletion mutant of Mycobacterium smegmatis Dps · the same entry in another collection · chain J against J, TM-score 1.00
A0R692 · AlphaFold monomer V2.0 prediction for DNA protection during starvation protein (A0R692) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 A0R692
Elsewhere: RCSB PDB 2YW7 · PDBe 2YW7 · UniProt A0R692

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