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Crystal structure of the second DNA-binding protein under starvation from mycobacterium smegmatis soaked with iron in the ratio of 360 iron atoms per dodecamer

Analyse Crystal structure of the second DNA-binding protein under starvation from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5WW7
Type: protein
Length: 642 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative starvation-induced DNA protecting PROTEIN/FERRITIN and dps
UniProt: A0QXB7
Ligands: FE2, FE, MG, CL
Pockets: 4 · best druggability 0.74

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Putative starvation-induced DNA protecting PROTEIN/FERRITIN and dps	protein	161	72% helix, 2% strand	A0QXB7
B, C	Putative starvation-induced DNA protecting PROTEIN/FERRITIN and dps	protein	160	73% helix, 3% strand	A0QXB7

Ligands and binding sites

FE2 · Fe (II) ion · metal · 5 copies · chains A, C, D
FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · 2 copies · chains A, B, C
CL · Chloride ion · ion · 2 copies · chains A, B, C

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	68	0.74	0.98	19	empty
2	61	0.72	0.98	17	empty
3	95	0.38	0.76	24	empty
4	57	0.33	0.77	13	empty

Interfaces

5 interfaces between chains.

C–D · 1434 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 1382 Å² buried · 22 hydrogen bonds · protein-protein
A–C · 1050 Å² buried · 23 hydrogen bonds · protein-protein
B–C · 555 Å² buried · 15 hydrogen bonds · protein-protein
A–D · 52 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

5WW7 · Crystal structure of the second DNA-Binding protein under starvation from Mycobacterium… · 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 A0QXB7
Elsewhere: RCSB PDB 5WW7 · PDBe 5WW7 · UniProt A0QXB7

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