MolNFT v1 · #70815 · protein

Crystal structure of ABC transporter, periplasmic substrate-binding protein SPO2066 from silicibacter pomeroyi

3LVU: “Crystal structure of ABC transporter, periplasmic substrate-binding protein SPO2066 from silicibacter pomeroyi”. X-ray diffraction, 1 ligand (IOD), 12 pockets (best druggability 0.81). MolNFT v1 #70815 on GenesisL1: 3D structure…

PDB: 3LVU
Type: protein
Length: 1,031 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ABC transporter, periplasmic substrate-binding protein
UniProt: Q5LRQ9
Ligands: IOD
Pockets: 12 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D	ABC transporter, periplasmic substrate-binding protein	protein	258	41% helix, 13% strand	Q5LRQ9
B	ABC transporter, periplasmic substrate-binding protein	protein	257	42% helix, 14% strand	Q5LRQ9

Ligands and binding sites

IOD · Iodide ion · ion · 14 copies · chains A, B, C, D
EDO · 1,2-ethanediol · additive · 5 copies · chains B, C
GOL · Glycerol · additive · 3 copies · chains A, B, C, D
PG5 · 1-methoxy-2-[2-(2-methoxy-ethoxy]-ethane · additive · 2 copies · chains B

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

Pockets

12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1123	0.81	0.82	132	IOD, EDO, GOL
2	344	0.58	0.76	39	empty
3	55	0.39	0.81	19	empty
4	111	0.37	0.74	22	IOD, EDO
5	101	0.35	0.74	16	empty

Interfaces

6 interfaces between chains.

B–C · 400 Å² buried · 6 hydrogen bonds · protein-protein
C–D · 394 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 366 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 187 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 87 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 modified (engineered).

Compared structures

3LVU · Crystal structure of ABC transporter, periplasmic substrate-binding protein SPO2066 from… · 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 Q5LRQ9
Elsewhere: RCSB PDB 3LVU · PDBe 3LVU · UniProt Q5LRQ9

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