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Crystal structure of cuss sensor domain with silver bound

Analyse Crystal structure of cuss sensor domain with silver bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5KU5
Type: protein
Length: 585 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sensor kinase cuss
EC: 2.7.13.3
UniProt: P77485
Ligands: AG
Pockets: 7 · best druggability 0.80

Structure

x-ray diffraction · 4 distinct chains · 36% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Sensor kinase cuss (EC 2.7.13.3)	protein	148	39% helix, 27% strand	P77485
B	Sensor kinase cuss (EC 2.7.13.3)	protein	146	36% helix, 26% strand	P77485
C	Sensor kinase cuss (EC 2.7.13.3)	protein	147	37% helix, 26% strand	P77485
D	Sensor kinase cuss (EC 2.7.13.3)	protein	144	31% helix, 27% strand	P77485

Ligands and binding sites

AG · Silver ion · metal · 8 copies · chains A, B, C, D
ACT · Acetate ion · additive · chains D

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

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	661	0.80	0.84	52	empty
2	624	0.79	0.84	48	empty
3	234	0.56	0.78	40	empty
4	77	0.42	0.80	15	empty
5	61	0.39	0.80	16	empty

Interfaces

5 interfaces between chains.

A–B · 688 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 627 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 367 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 265 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 199 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

5KU5 · Crystal Structure of CusS Sensor Domain with Silver Bound · the same entry in another collection · chain D against D, TM-score 1.00
P77485 · AlphaFold monomer V2.0 prediction for sensor histidine kinase cuss (P77485) · a predicted model of the same protein · chain D against A, TM-score 0.91

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 P77485
Elsewhere: RCSB PDB 5KU5 · PDBe 5KU5 · UniProt P77485

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