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Crystal structure of the phosphonate binding protein, phnd, from escherichia COLI

Analyse Crystal structure of the phosphonate binding protein, phnd, from escherichia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3QUJ
Type: protein
Length: 1,176 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phnd, subunit of alkylphosphonate ABC transporter
UniProt: Q1R3F7
Ligands: UNL
Pockets: 17 · best druggability 0.81

Structure

x-ray diffraction · 4 distinct chains · 50% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Phnd, subunit of alkylphosphonate ABC transporter	protein	301	51% helix, 22% strand	Q1R3F7
B	Phnd, subunit of alkylphosphonate ABC transporter	protein	304	51% helix, 21% strand	Q1R3F7
C	Phnd, subunit of alkylphosphonate ABC transporter	protein	284	50% helix, 20% strand	Q1R3F7
D	Phnd, subunit of alkylphosphonate ABC transporter	protein	287	49% helix, 22% strand	Q1R3F7

Ligands and binding sites

UNL · Unknown ligand · ligand · 4 copies · chains A, B, C, D

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

Pockets

17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	653	0.81	0.85	86	UNL
2	824	0.76	0.80	67	empty
3	364	0.75	0.86	51	empty
4	79	0.73	0.97	31	empty
5	157	0.66	0.87	33	UNL

Interfaces

5 interfaces between chains.

A–B · 1787 Å² buried · 14 hydrogen bonds · protein-protein
C–D · 1332 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 565 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 398 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 240 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 modified (engineered).

Compared structures

3QUJ · Crystal structure of the phosphonate binding protein, PhnD, from Escherichia coli · 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 Q1R3F7
Elsewhere: RCSB PDB 3QUJ · PDBe 3QUJ · UniProt Q1R3F7

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