Research workbench
Crystal structure of sugar aminotransferase wece with external aldimine VII from escherichia COLI K-12
Analyse Crystal structure of sugar aminotransferase wece with external aldimine VII… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZAH
- Type
- protein
- Length
- 2,946 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dtdp-4-amino-4,6-dideoxygalactose transaminase
- EC
- 2.6.1.59
- UniProt
- P27833
- Ligands
- T5K
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dtdp-4-amino-4,6-dideoxygalactose transaminase (EC 2.6.1.59) | protein | 370 | 40% helix, 17% strand | P27833 |
| C, H | Dtdp-4-amino-4,6-dideoxygalactose transaminase (EC 2.6.1.59) | protein | 368 | 42% helix, 17% strand | P27833 |
| D | Dtdp-4-amino-4,6-dideoxygalactose transaminase (EC 2.6.1.59) | protein | 369 | 41% helix, 17% strand | P27833 |
| E, F, G | Dtdp-4-amino-4,6-dideoxygalactose transaminase (EC 2.6.1.59) | protein | 367 | 40% helix, 16% strand | P27833 |
Ligands and binding sites
- T5K · [[(2R,3S,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3R,4S,5R,6R)-6-methyl-5-[(E)-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]-3,4-bis(oxidanyl)oxan-2-yl] hydrogen phosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 750 | 0.75 | 0.80 | 78 | empty |
| 2 | 566 | 0.75 | 0.82 | 58 | T5K |
| 3 | 461 | 0.75 | 0.83 | 60 | T5K |
| 4 | 473 | 0.74 | 0.83 | 61 | T5K |
| 5 | 408 | 0.74 | 0.84 | 56 | T5K |
Interfaces
16 interfaces between chains.
- A–B · 2330 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 2266 Ų buried · 23 hydrogen bonds · protein-protein
- G–H · 2263 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 2235 Ų buried · 25 hydrogen bonds · protein-protein
- B–G · 692 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4ZAH · Crystal structure of sugar aminotransferase WecE with External Aldimine VII from… · the same entry in another collection · chain E against E, TM-score 1.00
- P27833 · AlphaFold monomer V2.0 prediction for dtdp-4-amino-4,6-dideoxygalactose transaminase… · a predicted model of the same protein · chain C against A, TM-score 0.99
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 P27833
- Elsewhere: RCSB PDB 4ZAH · PDBe 4ZAH · UniProt P27833
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