MolNFT v1 · #177720 · protein

Crystal structure of D-allulose 3-epimerase from agrobacterium sp. SUL3

7ERM · D-tagatose 3-epimerase: “Crystal structure of D-allulose 3-epimerase from agrobacterium sp. SUL3”. X-ray diffraction, 2 ligands (MG, SO4), 13 pockets (best druggability 0.85). MolNFT v1 #177720 on GenesisL1: 3D structure, binding…

PDB: 7ERM
Type: protein
Length: 1,132 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: D-tagatose 3-epimerase
UniProt: A0A0L6K0Q2
Ligands: MG, SO4
Pockets: 13 · best druggability 0.85

Structure

x-ray diffraction · 1 distinct chain · 46% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	D-tagatose 3-epimerase	protein	283	46% helix, 15% strand	A0A0L6K0Q2

Ligands and binding sites

MG · Magnesium ion · metal · 5 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 4 copies · chains A, B, 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, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	577	0.85	0.91	66	empty
2	735	0.77	0.82	80	empty
3	419	0.70	0.81	53	empty
4	313	0.70	0.83	36	empty
5	263	0.55	0.77	39	empty

Interfaces

6 interfaces between chains.

A–B · 1692 Å² buried · 30 hydrogen bonds · protein-protein
C–D · 1666 Å² buried · 27 hydrogen bonds · protein-protein
A–C · 579 Å² buried · 4 hydrogen bonds · protein-protein
B–D · 564 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 391 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

7ERM · Crystal structure of D-allulose 3-epimerase from Agrobacterium sp. SUL3 · the same entry in another collection · chain A 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 A0A0L6K0Q2
Elsewhere: RCSB PDB 7ERM · PDBe 7ERM · UniProt A0A0L6K0Q2

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