MolNFT v1 · #49293 · protein

Crystal structure of D-mannonate dehydratase from novosphingobium aromaticivorans complexed with mg and 2-keto-3-deoxy-D-gluconate

2QJN · Mandelate RACEMASE/MUCONATE lactonizing enzyme: “Crystal structure of D-mannonate dehydratase from novosphingobium aromaticivorans complexed with mg and…”. X-ray diffraction, 2 ligands (KDG, MG), 12 pockets (best druggability 0.84).…

PDB: 2QJN
Type: protein
Length: 1,539 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mandelate RACEMASE/MUCONATE lactonizing enzyme
UniProt: A4XF23
Ligands: KDG, MG
Pockets: 12 · best druggability 0.84

Structure

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

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

Ligands and binding sites

KDG · 2-keto-3-deoxygluconate · 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

12 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	237	0.84	0.96	37	empty
2	459	0.83	0.91	59	empty
3	105	0.76	0.97	38	empty
4	278	0.74	0.88	37	empty
5	52	0.68	0.97	20	empty

Interfaces

5 interfaces between chains.

A–B · 2693 Å² buried · 30 hydrogen bonds · protein-protein
C–D · 2678 Å² buried · 31 hydrogen bonds · protein-protein
A–D · 1417 Å² buried · 27 hydrogen bonds · protein-protein
B–D · 1095 Å² buried · 21 hydrogen bonds · protein-protein
A–C · 1072 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

2QJN · Crystal structure of D-mannonate dehydratase from Novosphingobium aromaticivorans… · 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 C 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 2QJN · PDBe 2QJN · UniProt A4XF23

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