MolNFT v1 · #12071 · protein

1-deoxy-D-xylulose-5-phosphate reductoisomerase

1K5H: “1-deoxy-D-xylulose-5-phosphate reductoisomerase”. X-ray diffraction, 11 pockets (best druggability 0.77). MolNFT v1 #12071 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1K5H
Type: protein
Length: 1,187 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 1-deoxy-D-xylulose-5-phosphate reductoisomerase
EC: 1.1.1.-
UniProt: P45568
Pockets: 11 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 49% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	1-deoxy-D-xylulose-5-phosphate reductoisomerase (EC 1.1.1.-)	protein	398	50% helix, 15% strand	P45568
B	1-deoxy-D-xylulose-5-phosphate reductoisomerase (EC 1.1.1.-)	protein	391	48% helix, 15% strand	P45568

Pockets

11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	208	0.77	0.92	34	empty
2	725	0.76	0.81	69	empty
3	682	0.69	0.77	85	empty
4	578	0.66	0.76	66	empty
5	58	0.53	0.88	20	empty

Interfaces

2 interfaces between chains.

B–C · 1638 Å² buried · 31 hydrogen bonds · protein-protein
A–C · 1007 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

1K5H · 1-deoxy-D-xylulose-5-phosphate reductoisomerase · the same entry in another collection · chain B against B, TM-score 1.00
P45568 · AlphaFold monomer V2.0 prediction for 1-deoxy-D-xylulose 5-phosphate reductoisomerase… · a predicted model of the same protein · chain C against A, TM-score 0.93

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 P45568
Elsewhere: RCSB PDB 1K5H · PDBe 1K5H · UniProt P45568

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