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Structure of pseudo-centered cell crystal form of the C-terminal phosphatase domain of P. aeruginosa rssb

Analyse Structure of pseudo-centered cell crystal form of the C-terminal phosphatase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3F79
Type: protein
Length: 1,382 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Probable two-component response regulator
UniProt: Q9I045
Ligands: MG
Pockets: 20 · best druggability 0.75

Structure

x-ray diffraction · 6 distinct chains · 28% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Probable two-component response regulator	protein	223	29% helix, 30% strand	Q9I045
B	Probable two-component response regulator	protein	229	28% helix, 30% strand	Q9I045
C	Probable two-component response regulator	protein	229	28% helix, 29% strand	Q9I045
D	Probable two-component response regulator	protein	230	28% helix, 30% strand	Q9I045
E	Probable two-component response regulator	protein	236	28% helix, 29% strand	Q9I045
F	Probable two-component response regulator	protein	235	26% helix, 29% strand	Q9I045

Ligands and binding sites

MG · Magnesium ion · metal · 7 copies · chains B, C, D, E, F

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

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	93	0.75	0.96	22	empty
2	586	0.75	0.82	82	empty
3	141	0.75	0.93	29	empty
4	1143	0.74	0.77	102	MG
5	700	0.72	0.79	78	empty

Interfaces

8 interfaces between chains.

E–F · 1498 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 1454 Å² buried · 5 hydrogen bonds · protein-protein
C–D · 1359 Å² buried · 10 hydrogen bonds · protein-protein
B–D · 647 Å² buried · 4 hydrogen bonds · protein-protein
D–E · 556 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 34 modified (engineered).

Compared structures

3F79 · Structure of pseudo-centered cell crystal form of the C-terminal phosphatase domain of P.… · 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 Q9I045
Elsewhere: RCSB PDB 3F79 · PDBe 3F79 · UniProt Q9I045

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