Research workbench
Crystal structure of chloroflexus aurantiacus malyl-CoA lyase in complex with magnesium, oxalate, and propionyl-CoA
Analyse Crystal structure of chloroflexus aurantiacus malyl-CoA lyase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4L80
- Type
- protein
- Length
- 2,074 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HPCH/HPAI aldolase
- EC
- 4.1.3.24
- UniProt
- A9WC35
- Ligands
- 1VU, OXL, MG
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HPCH/HPAI aldolase (EC 4.1.3.24) | protein | 345 | 43% helix, 15% strand | A9WC35 |
| B, C, F | HPCH/HPAI aldolase (EC 4.1.3.24) | protein | 347 | 44% helix, 16% strand | A9WC35 |
| D, E | HPCH/HPAI aldolase (EC 4.1.3.24) | protein | 344 | 44% helix, 15% strand | A9WC35 |
Ligands and binding sites
- 1VU · propionyl Coenzyme A · ligand · 6 copies · chains A, C, B, D, F, E
- OXL · Oxalate ion · ligand · 6 copies · chains A, C, B, D, F, E
- MG · Magnesium ion · metal · 6 copies · chains A, C, B, D, F, E
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1014 | 0.80 | 0.82 | 123 | empty |
| 2 | 967 | 0.77 | 0.79 | 89 | empty |
| 3 | 924 | 0.76 | 0.79 | 84 | empty |
| 4 | 887 | 0.76 | 0.79 | 84 | empty |
| 5 | 907 | 0.76 | 0.79 | 87 | empty |
Interfaces
12 interfaces between chains.
- A–B · 2148 Ų buried · 27 hydrogen bonds · protein-protein
- E–F · 2143 Ų buried · 30 hydrogen bonds · protein-protein
- D–E · 2114 Ų buried · 26 hydrogen bonds · protein-protein
- D–F · 2113 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 2109 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 4L80 · Crystal Structure of Chloroflexus aurantiacus malyl-CoA lyase in complex with magnesium… · the same entry in another collection · chain F against F, TM-score 1.00
- A9WC35 · AlphaFold monomer V2.0 prediction for malyl-COA/BETA-methylmalyl- COA/CITRAMALYL-CoA… · a predicted model of the same protein · chain D 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 A9WC35
- Elsewhere: RCSB PDB 4L80 · PDBe 4L80 · UniProt A9WC35
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