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Structural genomics, the crystal structure of the C-terminal domain of histidine utilization repressor from pseudomonas syringae pv. tomato str. DC3000

Analyse Structural genomics, the crystal structure of the C-terminal domain of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2PKH
Type: protein
Length: 1,132 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histidine utilization repressor
UniProt: Q87UX0
Pockets: 17 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 19% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, F, G	Histidine utilization repressor	protein	141	21% helix, 50% strand	Q87UX0
B, C, E, H	Histidine utilization repressor	protein	142	18% helix, 51% strand	Q87UX0

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 32 copies · chains A, B, E, C, D, H, F, G

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

Pockets

17 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	955	0.82	0.84	106	EDO
2	625	0.78	0.84	70	EDO
3	323	0.74	0.87	42	EDO
4	350	0.74	0.86	49	empty
5	94	0.62	0.89	27	empty

Interfaces

20 interfaces between chains.

E–F · 1286 Å² buried · 23 hydrogen bonds · protein-protein
C–D · 1286 Å² buried · 23 hydrogen bonds · protein-protein
A–B · 1272 Å² buried · 24 hydrogen bonds · protein-protein
G–H · 1257 Å² buried · 24 hydrogen bonds · protein-protein
C–G · 583 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 modified (engineered).

Compared structures

2PKH · Structural Genomics, the crystal structure of the C-terminal domain of histidine… · 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 Q87UX0
Elsewhere: RCSB PDB 2PKH · PDBe 2PKH · UniProt Q87UX0

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