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Structural characterisation of nane, MANNAC6P C2 epimerase, from clostridium perfingens

Analyse Structural characterisation of nane, MANNAC6P C2 epimerase, from clostridium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4UTT
Type: protein
Length: 916 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative N-acetylmannosamine-6-phosphate 2-epimerase
EC: 5.1.3.9
UniProt: Q0TUP9
Ligands: CL
Pockets: 10 · best druggability 0.64

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Putative N-acetylmannosamine-6-phosphate 2-epimerase (EC 5.1.3.9)	protein	229	41% helix, 17% strand	Q0TUP9
C, D	Putative N-acetylmannosamine-6-phosphate 2-epimerase (EC 5.1.3.9)	protein	229	40% helix, 16% strand	Q0TUP9

Ligands and binding sites

CL · Chloride ion · ion · 8 copies · chains A, D, B, C
ACT · Acetate ion · additive · 4 copies · chains A, B, C, D

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

Pockets

10 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	418	0.64	0.78	59	empty
2	82	0.61	0.89	19	empty
3	229	0.61	0.81	32	CL, ACT
4	234	0.59	0.80	26	CL, ACT
5	216	0.58	0.80	25	CL, ACT

Interfaces

4 interfaces between chains.

A–D · 1639 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 364 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 200 Å² buried · 0 hydrogen bonds · protein-protein
A–C · 186 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

4UTT · Structural characterisation of NanE, ManNac6P C2 epimerase, from Clostridium perfingens · the same entry in another collection · chain A against A, TM-score 1.00
Q0TUP9 · AlphaFold monomer V2.0 prediction for putative N-acetylmannosamine-6-phosphate… · a predicted model of the same protein · chain A against A, TM-score 0.96

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 Q0TUP9
Elsewhere: RCSB PDB 4UTT · PDBe 4UTT · UniProt Q0TUP9

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