MolNFT v1 · #67230 · protein

Crystal structure of 3-keto-L-gulonate-6-phosphate decarboxylase from vibrio cholerae O1 biovar el tor str. N16961

3IEB · Hexulose-6-phosphate synthase sgbh: “Crystal structure of 3-keto-L-gulonate-6-phosphate decarboxylase from vibrio cholerae O1 biovar el tor str.…”. X-ray diffraction, 1 ligand (SO4), 8 pockets (best druggability 0.73). MolNFT v1…

PDB: 3IEB
Type: protein
Length: 1,068 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hexulose-6-phosphate synthase sgbh
UniProt: Q9KMS8
Ligands: SO4
Pockets: 8 · best druggability 0.73

Structure

x-ray diffraction · 3 distinct chains · 50% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hexulose-6-phosphate synthase sgbh	protein	213	50% helix, 21% strand	Q9KMS8
B, C, E	Hexulose-6-phosphate synthase sgbh	protein	214	50% helix, 21% strand	Q9KMS8
D	Hexulose-6-phosphate synthase sgbh	protein	213	50% helix, 21% strand	Q9KMS8

Ligands and binding sites

SO4 · Sulfate ion · ion · 17 copies · chains A, B, C, E, D
GOL · Glycerol · additive · 10 copies · chains A, B, D, C, E

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

Pockets

8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	748	0.73	0.79	63	GOL, SO4
2	515	0.70	0.80	51	GOL, SO4
3	518	0.69	0.79	64	SO4, GOL
4	512	0.67	0.78	68	GOL, SO4
5	525	0.67	0.78	56	GOL, SO4

Interfaces

5 interfaces between chains.

C–E · 1351 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 1337 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 519 Å² buried · 13 hydrogen bonds · protein-protein
A–C · 326 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 212 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 30 modified (engineered).

Compared structures

3IEB · Crystal structure of 3-keto-L-gulonate-6-phosphate decarboxylase from Vibrio cholerae O1… · 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 Q9KMS8
Elsewhere: RCSB PDB 3IEB · PDBe 3IEB · UniProt Q9KMS8

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