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Crystal structure of periplasmic binding protein from jonesia denitrificans

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

PDB: 4MLZ
Type: protein
Length: 598 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Periplasmic binding protein
UniProt: C7R301
Ligands: CA, K
Pockets: 5 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Periplasmic binding protein	protein	299	41% helix, 18% strand	C7R301
B	Periplasmic binding protein	protein	299	41% helix, 18% strand	C7R301

Ligands and binding sites

CA · Calcium ion · metal · 9 copies · chains A, B
K · Potassium ion · metal · 3 copies · chains A, B

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

Pockets

5 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	1009	0.78	0.80	70	empty
2	295	0.69	0.83	49	empty
3	340	0.66	0.80	34	empty
4	137	0.41	0.75	24	empty
5	76	0.33	0.74	17	empty

Interfaces

1 interface between chains.

A–B · 475 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 modified, 2 disulfide (engineered, disulfide).

Compared structures

4MLZ · Crystal structure of periplasmic binding protein from Jonesia denitrificans · 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 C7R301
Elsewhere: RCSB PDB 4MLZ · PDBe 4MLZ · UniProt C7R301

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