MolNFT v1 · #114584 · protein

Structure of the C-terminal domain of LPG1496 from legionella pneumophila in complex with nucleotide

5BU2: “Structure of the C-terminal domain of LPG1496 from legionella pneumophila in complex with nucleotide”. X-ray diffraction, 3 ligands (ADP, AMP, RIB), 11 pockets (best druggability 0.80). MolNFT v1 #114584 on GenesisL1: 3D structure…

PDB: 5BU2
Type: protein
Length: 1,157 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: LPG1496
UniProt: G8UY02
Ligands: ADP, AMP, RIB
Pockets: 11 · best druggability 0.80

Structure

x-ray diffraction · 3 distinct chains · 61% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	LPG1496	protein	288	63% helix, 2% strand	G8UY02
B, C	LPG1496	protein	290	62% helix, 3% strand	G8UY02
D	LPG1496	protein	289	60% helix, 2% strand	G8UY02

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C
AMP · Adenosine monophosphate · ligand · chains B, C
RIB · alpha-D-ribofuranose · ligand · chains D

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

Pockets

11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1178	0.80	0.81	105	ADP
2	252	0.79	0.91	30	AMP
3	809	0.77	0.81	91	RIB
4	600	0.69	0.78	47	ADP
5	324	0.66	0.81	38	ADP

Interfaces

5 interfaces between chains.

B–C · 646 Å² buried · 11 hydrogen bonds · protein-protein
B–D · 533 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 518 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 500 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 226 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

5BU2 · Structure of the C-terminal domain of lpg1496 from Legionella pneumophila in complex with… · 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 G8UY02
Elsewhere: RCSB PDB 5BU2 · PDBe 5BU2 · UniProt G8UY02

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