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Crystal structure of an ider-DNA complex reveals a conformational change in activated ider for base-specific interactions

Analyse Crystal structure of an ider-DNA complex reveals a conformational change in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1U8R
Type: protein + DNA
Length: 1,902 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mbta operator DNA; Mbtb operator DNA; Iron-dependent repressor ider
UniProt: P0A672
Ligands: CO, NA
Pockets: 20 · best druggability 0.70

Structure

x-ray diffraction · 4 distinct chains · 48% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E, K	Mbta operator DNA	dna	33	—	—
F, L	Mbtb operator DNA	dna	33	—	—
A, B, C, D, G, I	Iron-dependent repressor ider	protein	221	49% helix, 16% strand	P0A672
H, J	Iron-dependent repressor ider	protein	222	46% helix, 16% strand	P0A672

Ligands and binding sites

CO · Cobalt (II) ion · metal · 24 copies · chains A, B, C, D, G, H, I, J
NA · Sodium ion · metal · 8 copies · chains F, A, E, B, C, D, L, G, K, H, I, J

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	901	0.70	0.76	73	empty
2	881	0.70	0.76	73	empty
3	204	0.53	0.78	28	empty
4	228	0.52	0.76	32	empty
5	201	0.52	0.77	28	empty

Interfaces

27 interfaces between chains.

E–F · 1467 Å² buried · 116 hydrogen bonds · nucleic-nucleic
K–L · 1467 Å² buried · 118 hydrogen bonds · nucleic-nucleic
C–D · 989 Å² buried · 18 hydrogen bonds · protein-protein
G–H · 988 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 985 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

1U8R · Crystal Structure of an IdeR-DNA Complex Reveals a Conformational Change in Activated… · the same entry in another collection · chain E against E, 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 P0A672
Elsewhere: RCSB PDB 1U8R · PDBe 1U8R · UniProt P0A672

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