MolNFT v1 · #176836 · protein
Crystal structures of D-allulose 3-epimerase with D-tagatose from sinorhizobium fredii
7DZ4 · D-tagatose 3-epimerase: “Crystal structures of D-allulose 3-epimerase with D-tagatose from sinorhizobium fredii”. X-ray diffraction, 2 ligands (TAG, MG), 13 pockets (best druggability 0.87). MolNFT v1 #176836 on GenesisL1: 3D…
- PDB
- 7DZ4
- Type
- protein
- Length
- 1,138 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-tagatose 3-epimerase
- EC
- 5.1.3.-
- UniProt
- A0A249Q1V1
- Ligands
- TAG, MG
- Pockets
- 13 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-tagatose 3-epimerase (EC 5.1.3.-) | protein | 284 | 45% helix, 15% strand | A0A249Q1V1 |
| B | D-tagatose 3-epimerase (EC 5.1.3.-) | protein | 283 | 46% helix, 15% strand | A0A249Q1V1 |
| C | D-tagatose 3-epimerase (EC 5.1.3.-) | protein | 286 | 47% helix, 15% strand | A0A249Q1V1 |
| D | D-tagatose 3-epimerase (EC 5.1.3.-) | protein | 285 | 46% helix, 15% strand | A0A249Q1V1 |
Ligands and binding sites
- TAG · D-tagatose · ligand · 2 copies · chains C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 583 | 0.87 | 0.93 | 56 | empty |
| 2 | 71 | 0.75 | 0.99 | 23 | TAG |
| 3 | 66 | 0.73 | 0.98 | 24 | TAG |
| 4 | 263 | 0.69 | 0.85 | 34 | empty |
| 5 | 309 | 0.68 | 0.83 | 44 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1648 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 1635 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 568 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 565 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 436 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7DZ4 · Crystal structures of D-allulose 3-epimerase with D-tagatose from Sinorhizobium fredii · 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 A0A249Q1V1
- Elsewhere: RCSB PDB 7DZ4 · PDBe 7DZ4 · UniProt A0A249Q1V1
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