MolNFT v1 · #177012 · protein

Crystal structure of lactobacillus rhamnosus 4-deoxy-L-threo-5- hexosulose-uronate ketol-isomerase kdui complexed with hepes

7E4S · 5-dehydro-4-deoxy-D-glucuronate isomerase: “Crystal structure of lactobacillus rhamnosus 4-deoxy-L-threo-5- hexosulose-uronate ketol-isomerase kdui…”. X-ray diffraction, 1 ligand (ZN), 17 pockets (best druggability 0.72). MolNFT v1…

PDB: 7E4S
Type: protein
Length: 1,646 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5-dehydro-4-deoxy-D-glucuronate isomerase
EC: 5.3.1.17
UniProt: A0A508YKK7
Ligands: ZN
Pockets: 17 · best druggability 0.72

Structure

x-ray diffraction · 3 distinct chains · 7% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, F	5-dehydro-4-deoxy-D-glucuronate isomerase (EC 5.3.1.17)	protein	279	7% helix, 43% strand	A0A508YKK7
D	5-dehydro-4-deoxy-D-glucuronate isomerase (EC 5.3.1.17)	protein	260	7% helix, 41% strand	A0A508YKK7
E	5-dehydro-4-deoxy-D-glucuronate isomerase (EC 5.3.1.17)	protein	270	7% helix, 44% strand	A0A508YKK7

Ligands and binding sites

ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 6 copies · chains A, B, C, D, E, F

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

Pockets

17 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	74	0.72	0.96	21	empty
2	68	0.71	0.97	18	empty
3	267	0.66	0.82	21	EPE
4	50	0.65	0.95	14	empty
5	250	0.62	0.80	24	EPE

Interfaces

6 interfaces between chains.

B–C · 1638 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 1628 Å² buried · 41 hydrogen bonds · protein-protein
E–F · 1615 Å² buried · 41 hydrogen bonds · protein-protein
A–E · 1607 Å² buried · 22 hydrogen bonds · protein-protein
C–D · 1595 Å² buried · 36 hydrogen bonds · protein-protein

Compared structures

7E4S · Crystal structure of Lactobacillus rhamnosus 4-deoxy-L-threo-5-hexosulose-uronate… · 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 A0A508YKK7
Elsewhere: RCSB PDB 7E4S · PDBe 7E4S · UniProt A0A508YKK7

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