Research workbench
Crystal structure of ethanolamine ammonia-lyase heavy chain (YP_013784.1) from listeria monocytogenes 4B F2365 at 2.15 a resolution
Analyse Crystal structure of ethanolamine ammonia-lyase heavy chain (YP_013784.1) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QEZ
- Type
- protein
- Length
- 2,628 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ethanolamine ammonia-lyase heavy chain
- EC
- 4.3.1.7
- UniProt
- Q720Q3
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ethanolamine ammonia-lyase heavy chain (EC 4.3.1.7) | protein | 439 | 49% helix, 13% strand | Q720Q3 |
| B | Ethanolamine ammonia-lyase heavy chain (EC 4.3.1.7) | protein | 437 | 48% helix, 14% strand | Q720Q3 |
| C | Ethanolamine ammonia-lyase heavy chain (EC 4.3.1.7) | protein | 437 | 49% helix, 13% strand | Q720Q3 |
| D | Ethanolamine ammonia-lyase heavy chain (EC 4.3.1.7) | protein | 438 | 50% helix, 14% strand | Q720Q3 |
| E | Ethanolamine ammonia-lyase heavy chain (EC 4.3.1.7) | protein | 434 | 50% helix, 13% strand | Q720Q3 |
| F | Ethanolamine ammonia-lyase heavy chain (EC 4.3.1.7) | protein | 443 | 49% helix, 13% strand | Q720Q3 |
Ligands and binding sites
- GOL · Glycerol · additive · 6 copies · chains A, F, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1021 | 0.81 | 0.83 | 84 | empty |
| 2 | 965 | 0.81 | 0.83 | 84 | empty |
| 3 | 929 | 0.81 | 0.83 | 83 | empty |
| 4 | 107 | 0.76 | 0.96 | 23 | empty |
| 5 | 101 | 0.76 | 0.96 | 24 | GOL |
Interfaces
6 interfaces between chains.
- A–F · 1565 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 1553 Ų buried · 29 hydrogen bonds · protein-protein
- D–E · 1492 Ų buried · 30 hydrogen bonds · protein-protein
- C–F · 936 Ų buried · 29 hydrogen bonds · protein-protein
- B–D · 909 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 89 modified (engineered).
Compared structures
- 2QEZ · Crystal structure of ethanolamine ammonia-lyase heavy chain (YP_013784.1) from Listeria… · 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 Q720Q3
- Elsewhere: RCSB PDB 2QEZ · PDBe 2QEZ · UniProt Q720Q3
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