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Crystal structure of the periplasmic lipopolysaccharide transport protein lpta (yhbn), trigonal form

Analyse Crystal structure of the periplasmic lipopolysaccharide transport protein lpta… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2R1A
Type: protein
Length: 1,066 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein yhbn
UniProt: P0ADV1
Pockets: 12 · best druggability 0.70

Structure

x-ray diffraction · 8 distinct chains · 1% helix, 54% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein yhbn	protein	131	2% helix, 43% strand	P0ADV1
B	Protein yhbn	protein	134	0% helix, 58% strand	P0ADV1
C	Protein yhbn	protein	135	0% helix, 62% strand	P0ADV1
D	Protein yhbn	protein	136	0% helix, 49% strand	P0ADV1
E	Protein yhbn	protein	132	0% helix, 53% strand	P0ADV1
F	Protein yhbn	protein	132	0% helix, 55% strand	P0ADV1
G	Protein yhbn	protein	135	0% helix, 58% strand	P0ADV1
H	Protein yhbn	protein	131	2% helix, 56% strand	P0ADV1

Pockets

12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	313	0.70	0.84	55	empty
2	199	0.66	0.85	45	empty
3	124	0.65	0.88	30	empty
4	157	0.65	0.86	28	empty
5	528	0.63	0.76	52	empty

Interfaces

7 interfaces between chains.

G–H · 812 Å² buried · 20 hydrogen bonds · protein-protein
B–C · 795 Å² buried · 15 hydrogen bonds · protein-protein
C–D · 792 Å² buried · 12 hydrogen bonds · protein-protein
E–F · 788 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 777 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

2R1A · Crystal structure of the periplasmic lipopolysaccharide transport protein LptA (YhbN)… · the same entry in another collection · chain E against E, TM-score 1.00
P0ADV1 · AlphaFold monomer V2.0 prediction for lipopolysaccharide export system protein lpta… · a predicted model of the same protein · chain C against A, TM-score 0.98

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 P0ADV1
Elsewhere: RCSB PDB 2R1A · PDBe 2R1A · UniProt P0ADV1

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