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Crystal structure of the K271E mutant of mannonate dehydratase from novosphingobium aromaticivorans complexed with mg and D-mannonate

Analyse Crystal structure of the K271E mutant of mannonate dehydratase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2QJM
Type: protein
Length: 1,538 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mandelate RACEMASE/MUCONATE lactonizing enzyme
UniProt: A4XF23
Ligands: CS2, MG
Pockets: 13 · best druggability 0.88

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Mandelate RACEMASE/MUCONATE lactonizing enzyme	protein	384	40% helix, 20% strand	A4XF23
B, D	Mandelate RACEMASE/MUCONATE lactonizing enzyme	protein	385	40% helix, 20% strand	A4XF23

Ligands and binding sites

CS2 · D-mannonic acid · ligand · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · 4 copies · chains A, B, C, D

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	714	0.88	0.92	100	empty
2	124	0.79	0.97	44	empty
3	112	0.77	0.97	35	empty
4	269	0.74	0.88	36	empty
5	339	0.64	0.80	54	empty

Interfaces

5 interfaces between chains.

A–B · 2669 Å² buried · 33 hydrogen bonds · protein-protein
C–D · 2656 Å² buried · 28 hydrogen bonds · protein-protein
A–D · 1394 Å² buried · 24 hydrogen bonds · protein-protein
A–C · 1086 Å² buried · 19 hydrogen bonds · protein-protein
B–D · 1049 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

2QJM · Crystal structure of the K271E mutant of Mannonate dehydratase from Novosphingobium… · the same entry in another collection · chain A against A, TM-score 1.00
A4XF23 · AlphaFold monomer V2.0 prediction for D-mannonate dehydratase (A4XF23) · a predicted model of the same protein · chain B 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 A4XF23
Elsewhere: RCSB PDB 2QJM · PDBe 2QJM · UniProt A4XF23

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