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Crystal structure of yfau, a metal ion dependent class II aldolase from escherichia COLI K12 - mg-pyruvate product complex

Analyse Crystal structure of yfau, a metal ion dependent class II aldolase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2VWT
Type: protein
Length: 768 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Yfau, 2-keto-3-deoxy sugar aldolase
EC: 4.1.2.20
UniProt: P76469
Ligands: PYR, MG, PO4
Pockets: 13 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 46% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Yfau, 2-keto-3-deoxy sugar aldolase (EC 4.1.2.20)	protein	256	46% helix, 16% strand	P76469

Ligands and binding sites

PYR · Pyruvic acid · ligand · 3 copies · chains A, B, C
MG · Magnesium ion · metal · 3 copies · chains A, B, C
PO4 · Phosphate ion · ion · 3 copies · chains A, B, C
GOL · Glycerol · additive · chains C

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

Pockets

13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	451	0.82	0.89	41	empty
2	414	0.70	0.81	64	MG, PYR
3	368	0.69	0.82	44	MG, PYR
4	368	0.68	0.81	45	MG, PYR
5	151	0.58	0.83	30	empty

Interfaces

3 interfaces between chains.

B–C · 933 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 931 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 922 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

2VWT · Crystal structure of YfaU, a metal ion dependent class II aldolase from Escherichia coli… · the same entry in another collection · chain A against A, TM-score 1.00
P76469 · AlphaFold monomer V2.0 prediction for 2-keto-3-deoxy-L-rhamnonate aldolase (P76469) · a predicted model of the same protein · chain A 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 P76469
Elsewhere: RCSB PDB 2VWT · PDBe 2VWT · UniProt P76469

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