MolNFT v1 · #16672 · protein

Crystal structure of kdo-8-phosphate synthase

1O60 · 2-dehydro-3-deoxyphosphooctonate aldolase: “Crystal structure of kdo-8-phosphate synthase”. X-ray diffraction, 14 pockets (best druggability 0.76). MolNFT v1 #16672 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1O60
Type: protein
Length: 1,076 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 2-dehydro-3-deoxyphosphooctonate aldolase
EC: 2.5.1.55
UniProt: P45251
Pockets: 14 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55)	protein	269	42% helix, 21% strand	P45251

Pockets

14 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	579	0.76	0.83	49	empty
2	580	0.74	0.81	53	empty
3	611	0.74	0.81	51	empty
4	575	0.73	0.81	48	empty
5	141	0.67	0.88	30	empty

Interfaces

6 interfaces between chains.

A–C · 1580 Å² buried · 28 hydrogen bonds · protein-protein
A–B · 1578 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 1483 Å² buried · 13 hydrogen bonds · protein-protein
B–D · 1477 Å² buried · 24 hydrogen bonds · protein-protein
B–C · 214 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 36 modified (engineered).

Compared structures

1O60 · Crystal structure of KDO-8-phosphate synthase · the same entry in another collection · chain B against B, TM-score 1.00
P45251 · AlphaFold monomer V2.0 prediction for 2-dehydro-3-deoxyphosphooctonate aldolase (P45251) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P45251
Elsewhere: RCSB PDB 1O60 · PDBe 1O60 · UniProt P45251

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