MolNFT v1 · #62501 · protein

Crystal structure of deskc in complex with AMP-pcp

3EHF · Sensor kinase (yocf protein): “Crystal structure of deskc in complex with AMP-pcp”. X-ray diffraction, 2 ligands (ACP, MG), 4 pockets (best druggability 0.55). MolNFT v1 #62501 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 3EHF
Type: protein
Length: 521 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sensor kinase (yocf protein)
EC: 2.7.13.3
UniProt: O34757
Ligands: ACP, MG
Pockets: 4 · best druggability 0.55

Structure

x-ray diffraction · 4 distinct chains · 66% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Sensor kinase (yocf protein) (EC 2.7.13.3)	protein	179	58% helix, 18% strand	O34757
B	Sensor kinase (yocf protein) (EC 2.7.13.3)	protein	104	79% helix, 2% strand	O34757
C	Sensor kinase (yocf protein) (EC 2.7.13.3)	protein	57	89% helix, 0% strand	O34757
D	Sensor kinase (yocf protein) (EC 2.7.13.3)	protein	181	59% helix, 18% strand	O34757

Ligands and binding sites

ACP · Phosphomethylphosphonic acid adenylate ester · ligand · 3 copies · chains A, B, D
MG · Magnesium ion · metal · 3 copies · chains A, B, D

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	82	0.55	0.86	20	ACP
2	63	0.51	0.86	17	ACP
3	100	0.33	0.73	21	empty
4	51	0.27	0.74	14	empty

Interfaces

4 interfaces between chains.

A–B · 1520 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 1328 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 125 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 109 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 14 modified (engineered).

Compared structures

3EHF · Crystal structure of DesKC in complex with AMP-PCP · the same entry in another collection · chain D against D, TM-score 1.00
O34757 · AlphaFold monomer V2.0 prediction for sensor histidine kinase desk (O34757) · a predicted model of the same protein · chain C against A, TM-score 0.93

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 O34757
Elsewhere: RCSB PDB 3EHF · PDBe 3EHF · UniProt O34757

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