Research workbench
2.35 ångström resolution crystal structure of putative O- acetylhomoserine (thiol)-lyase (mety) from campylobacter jejuni subsp. jejuni nctc 11168 with N'-pyridoxyl-lysine-5'-monophosphate at position 205
Analyse 2.35 ångström resolution crystal structure of putative O- acetylhomoserine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OC9
- Type
- protein
- Length
- 6,624 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative O-acetylhomoserine (thiol)-lyase
- EC
- 2.5.1.49
- UniProt
- Q0P7Q4
- Ligands
- PO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 8 distinct chains · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Putative O-acetylhomoserine (thiol)-lyase (EC 2.5.1.49) | protein | 421 | 40% helix, 15% strand | Q0P7Q4 |
| B | Putative O-acetylhomoserine (thiol)-lyase (EC 2.5.1.49) | protein | 421 | 40% helix, 15% strand | Q0P7Q4 |
| D, F, G, H | Putative O-acetylhomoserine (thiol)-lyase (EC 2.5.1.49) | protein | 422 | 40% helix, 15% strand | Q0P7Q4 |
| I | Putative O-acetylhomoserine (thiol)-lyase (EC 2.5.1.49) | protein | 403 | 40% helix, 16% strand | Q0P7Q4 |
| J, L, M | Putative O-acetylhomoserine (thiol)-lyase (EC 2.5.1.49) | protein | 407 | 39% helix, 16% strand | Q0P7Q4 |
| K | Putative O-acetylhomoserine (thiol)-lyase (EC 2.5.1.49) | protein | 406 | 40% helix, 16% strand | Q0P7Q4 |
| N, O | Putative O-acetylhomoserine (thiol)-lyase (EC 2.5.1.49) | protein | 405 | 40% helix, 16% strand | Q0P7Q4 |
| P | Putative O-acetylhomoserine (thiol)-lyase (EC 2.5.1.49) | protein | 412 | 40% helix, 16% strand | Q0P7Q4 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · chains C
- GOL · Glycerol · additive · 3 copies · chains A, D, B, G, O
- IMD · Imidazole · additive · 2 copies · chains A, D
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 | 1118 | 0.83 | 0.84 | 110 | GOL |
| 2 | 760 | 0.76 | 0.81 | 79 | empty |
| 3 | 917 | 0.76 | 0.79 | 87 | empty |
| 4 | 892 | 0.76 | 0.80 | 87 | empty |
| 5 | 736 | 0.76 | 0.81 | 76 | empty |
Interfaces
34 interfaces between chains.
- E–F · 3151 Ų buried · 56 hydrogen bonds · protein-protein
- A–D · 3127 Ų buried · 53 hydrogen bonds · protein-protein
- G–H · 3119 Ų buried · 52 hydrogen bonds · protein-protein
- B–C · 3113 Ų buried · 50 hydrogen bonds · protein-protein
- M–N · 2631 Ų buried · 39 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified (cofactor, engineered).
Compared structures
- 4OC9 · 2.35 Angstrom resolution crystal structure of putative O-acetylhomoserine (thiol)-lyase… · 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 Q0P7Q4
- Elsewhere: RCSB PDB 4OC9 · PDBe 4OC9 · UniProt Q0P7Q4
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