MolNFT v1 · #125465 · protein

Crystal structure of the pbp mota from a. tumefaciens B6

5L9P · Periplasmic binding protein: “Crystal structure of the pbp mota from a. tumefaciens B6”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.64). MolNFT v1 #125465 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 5L9P
Type: protein
Length: 682 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Periplasmic binding protein
UniProt: A0A109C781
Ligands: SO4
Pockets: 4 · best druggability 0.64

Structure

x-ray diffraction · 2 distinct chains · 45% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Periplasmic binding protein	protein	340	45% helix, 20% strand	A0A109C781
B	Periplasmic binding protein	protein	342	44% helix, 20% strand	A0A109C781

Ligands and binding sites

SO4 · Sulfate ion · ion · 12 copies · chains A, B

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

Pockets

4 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	467	0.64	0.77	60	SO4
2	475	0.63	0.76	56	empty
3	418	0.61	0.76	53	empty
4	191	0.46	0.74	23	SO4

Interfaces

1 interface between chains.

A–B · 712 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

5L9P · Crystal structure of the PBP MotA from A. tumefaciens B6 · 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 A0A109C781
Elsewhere: RCSB PDB 5L9P · PDBe 5L9P · UniProt A0A109C781

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