MolNFT v1 · #48228 · protein

Crystal structure of the DNA-binding domain of phop

2PMU · Response regulator phop: “Crystal structure of the DNA-binding domain of phop”. X-ray diffraction, 5 ligands (GLY, K, PO4), 7 pockets (best druggability 0.48). MolNFT v1 #48228 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 2PMU
Type: protein
Length: 585 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Response regulator phop
UniProt: P71814
Ligands: GLY, K, PO4, UNX, CL
Pockets: 7 · best druggability 0.48

Structure

x-ray diffraction · 5 distinct chains · 35% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Response regulator phop	protein	98	34% helix, 23% strand	P71814
B, E	Response regulator phop	protein	103	34% helix, 22% strand	P71814
C	Response regulator phop	protein	92	37% helix, 26% strand	P71814
D	Response regulator phop	protein	96	35% helix, 24% strand	P71814
F	Response regulator phop	protein	93	38% helix, 26% strand	P71814

Ligands and binding sites

GLY · Glycine · ligand · 3 copies · chains B, C, E
K · Potassium ion · metal · 3 copies · chains A, D, E
PO4 · Phosphate ion · ion · 4 copies · chains A, D, E
UNX · Unknown atom or ion · ion · 4 copies · chains A, B, D, E
CL · Chloride ion · ion · 4 copies · chains B, C, D, E, F

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

Pockets

7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	148	0.48	0.78	29	empty
2	113	0.46	0.79	16	empty
3	107	0.43	0.77	16	empty
4	79	0.38	0.77	18	GLY
5	79	0.36	0.76	19	empty

Interfaces

6 interfaces between chains.

B–C · 519 Å² buried · 10 hydrogen bonds · protein-protein
E–F · 514 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 512 Å² buried · 9 hydrogen bonds · protein-protein
A–F · 449 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 435 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

2PMU · Crystal structure of the DNA-binding domain of PhoP · 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 P71814
Elsewhere: RCSB PDB 2PMU · PDBe 2PMU · UniProt P71814

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