MolNFT v1 · #108008 · protein
Structural characterisation of nane, MANNAC6P C2 epimerase, from clostridium perfingens
4UTT · Putative N-acetylmannosamine-6-phosphate 2-epimerase: “Structural characterisation of nane, MANNAC6P C2 epimerase, from clostridium perfingens”. X-ray diffraction, 1 ligand (CL), 10 pockets (best druggability 0.64). MolNFT v1…
- 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.
| Volume (ų) | 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 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 364 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 200 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 186 Ų 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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