Research workbench
Crystal structure of sugar aminotransferase wece from escherichia COLI K-12
Analyse Crystal structure of sugar aminotransferase wece from escherichia COLI K-12 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PIW
- Type
- protein
- Length
- 2,888 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tdp-4-keto-6-deoxy-D-glucose transaminase family protein
- UniProt
- N2U028
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tdp-4-keto-6-deoxy-D-glucose transaminase family protein | protein | 360 | 40% helix, 16% strand | N2U028 |
| B, E | Tdp-4-keto-6-deoxy-D-glucose transaminase family protein | protein | 362 | 40% helix, 17% strand | N2U028 |
| C | Tdp-4-keto-6-deoxy-D-glucose transaminase family protein | protein | 362 | 41% helix, 17% strand | N2U028 |
| D | Tdp-4-keto-6-deoxy-D-glucose transaminase family protein | protein | 361 | 41% helix, 17% strand | N2U028 |
| F | Tdp-4-keto-6-deoxy-D-glucose transaminase family protein | protein | 359 | 39% helix, 16% strand | N2U028 |
| G, H | Tdp-4-keto-6-deoxy-D-glucose transaminase family protein | protein | 361 | 40% helix, 17% strand | N2U028 |
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 124 | 0.79 | 0.97 | 26 | empty |
| 2 | 77 | 0.74 | 0.98 | 14 | empty |
| 3 | 71 | 0.74 | 0.98 | 17 | empty |
| 4 | 69 | 0.72 | 0.97 | 17 | empty |
| 5 | 937 | 0.69 | 0.74 | 72 | empty |
Interfaces
12 interfaces between chains.
- A–B · 2017 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 2001 Ų buried · 26 hydrogen bonds · protein-protein
- E–F · 1898 Ų buried · 23 hydrogen bonds · protein-protein
- G–H · 1748 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 186 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 100 modified (engineered, cofactor).
Compared structures
- 4PIW · Crystal structure of sugar aminotransferase WecE from Escherichia coli K-12 · 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 N2U028
- Elsewhere: RCSB PDB 4PIW · PDBe 4PIW · UniProt N2U028
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