Research workbench
Crystal structure of rhodobacter sphaeroides malyl-CoA lyase in complex with magnesium, oxalate, and CoA
Analyse Crystal structure of rhodobacter sphaeroides 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
- 4L9Z
- Type
- protein
- Length
- 1,881 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malyl-CoA lyase
- EC
- 4.1.3.24
- UniProt
- Q3J5L6
- Ligands
- COA, OXL, MG
- Pockets
- 15 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, F | Malyl-CoA lyase (EC 4.1.3.24) | protein | 313 | 46% helix, 18% strand | Q3J5L6 |
| B, C, D | Malyl-CoA lyase (EC 4.1.3.24) | protein | 314 | 46% helix, 18% strand | Q3J5L6 |
Ligands and binding sites
- COA · 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, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 909 | 0.76 | 0.79 | 104 | empty |
| 2 | 881 | 0.76 | 0.80 | 104 | empty |
| 3 | 917 | 0.76 | 0.79 | 97 | empty |
| 4 | 891 | 0.75 | 0.79 | 107 | empty |
| 5 | 870 | 0.75 | 0.79 | 99 | empty |
Interfaces
12 interfaces between chains.
- B–C · 2255 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 2249 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 2235 Ų buried · 35 hydrogen bonds · protein-protein
- D–E · 2234 Ų buried · 32 hydrogen bonds · protein-protein
- E–F · 2210 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 4L9Z · Crystal Structure of Rhodobacter sphaeroides malyl-CoA lyase in complex with magnesium… · the same entry in another collection · chain F against F, TM-score 1.00
- Q3J5L6 · AlphaFold monomer V2.0 prediction for L-malyl-COA/BETA-methylmalyl- CoA lyase (Q3J5L6) · a predicted model of the same protein · chain B 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 Q3J5L6
- Elsewhere: RCSB PDB 4L9Z · PDBe 4L9Z · UniProt Q3J5L6
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