MolNFT v1 · #70463 · protein

X-ray structures of isopentenyl phosphate kinase

3LL9: “X-ray structures of isopentenyl phosphate kinase”. X-ray diffraction, 1 ligand (ADP), 5 pockets (best druggability 0.60). MolNFT v1 #70463 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3LL9
Type: protein
Length: 493 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Isopentenyl phosphate kinase
UniProt: O26153
Ligands: ADP
Pockets: 5 · best druggability 0.60

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Isopentenyl phosphate kinase	protein	244	41% helix, 23% strand	O26153
B	Isopentenyl phosphate kinase	protein	249	40% helix, 24% strand	O26153

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
GOL · Glycerol · additive · chains 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	372	0.60	0.77	52	GOL, ADP
2	218	0.54	0.77	34	ADP
3	83	0.42	0.79	20	empty
4	68	0.34	0.76	17	empty
5	77	0.33	0.75	18	empty

Interfaces

1 interface between chains.

A–B · 1671 Å² buried · 36 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 modified (engineered).

Compared structures

3LL9 · X-ray structures of isopentenyl phosphate kinase · the same entry in another collection · chain A against A, TM-score 1.00
O26153 · AlphaFold monomer V2.0 prediction for isopentenyl phosphate kinase (O26153) · a predicted model of the same protein · chain B 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 O26153
Elsewhere: RCSB PDB 3LL9 · PDBe 3LL9 · UniProt O26153

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