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Crystal structure of the GDP-D-glycero-4-keto-D-lyxo-heptose-3,5- epimerase from campylobacter jejuni, serotype HS:15

Analyse Crystal structure of the GDP-D-glycero-4-keto-D-lyxo-heptose-3,5- epimerase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 8DB5
Type: protein
Length: 1,412 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GDP-D-glycero-4-keto-D-lyxo-heptose-3,5-epimerase
EC: 5.1.3.13
UniProt: A0A0S2CFK0
Ligands: GDP, CL
Pockets: 16 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 8% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D, F, G, H	GDP-D-glycero-4-keto-D-lyxo-heptose-3,5-epimerase (EC 5.1.3.13)	protein	176	9% helix, 48% strand	A0A0S2CFK0
B, E	GDP-D-glycero-4-keto-D-lyxo-heptose-3,5-epimerase (EC 5.1.3.13)	protein	178	8% helix, 47% strand	A0A0S2CFK0

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
CL · Chloride ion · ion · 7 copies · chains A, B, D, E, F, G, H

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

Pockets

16 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	1038	0.81	0.83	102	GDP, CL
2	1043	0.74	0.77	90	empty
3	313	0.73	0.86	46	GDP, CL
4	270	0.71	0.86	32	CL, GDP
5	317	0.70	0.84	42	GDP, CL

Interfaces

11 interfaces between chains.

E–F · 1685 Å² buried · 34 hydrogen bonds · protein-protein
G–H · 1680 Å² buried · 33 hydrogen bonds · protein-protein
A–B · 1676 Å² buried · 34 hydrogen bonds · protein-protein
C–D · 1650 Å² buried · 36 hydrogen bonds · protein-protein
B–F · 656 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

8DB5 · Crystal structure of the GDP-D-glycero-4-keto-d-lyxo-heptose-3,5-epimerase from… · the same entry in another collection · chain H against H, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt A0A0S2CFK0
Elsewhere: RCSB PDB 8DB5 · PDBe 8DB5 · UniProt A0A0S2CFK0

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