MolNFT v1 · #98453 · protein
Crystal structure of rhodobacter sphaeroides malyl-CoA lyase in complex with magnesium, glyoxylate, and propionyl-CoA
4L9Y: “Crystal structure of rhodobacter sphaeroides malyl-CoA lyase in complex with magnesium, glyoxylate, and…”. X-ray diffraction, 4 ligands (GLV, 1VU, MG), 20 pockets (best druggability 0.82). MolNFT v1 #98453 on GenesisL1: 3D…
- PDB
- 4L9Y
- Type
- protein
- Length
- 1,733 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
- GLV, 1VU, MG, CL
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Malyl-CoA lyase (EC 4.1.3.24) | protein | 314 | 45% helix, 17% strand | Q3J5L6 |
| B | Malyl-CoA lyase (EC 4.1.3.24) | protein | 264 | 42% helix, 18% strand | Q3J5L6 |
| C | Malyl-CoA lyase (EC 4.1.3.24) | protein | 316 | 45% helix, 16% strand | Q3J5L6 |
| D, E | Malyl-CoA lyase (EC 4.1.3.24) | protein | 265 | 41% helix, 18% strand | Q3J5L6 |
| F | Malyl-CoA lyase (EC 4.1.3.24) | protein | 309 | 45% helix, 18% strand | Q3J5L6 |
Ligands and binding sites
- GLV · Glyoxylic acid · ligand · 2 copies · chains A, B, D, F
- 1VU · propionyl Coenzyme A · ligand · chains A, B
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, F, E
- CL · Chloride ion · ion · 4 copies · chains A, C, 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 917 | 0.82 | 0.84 | 111 | CL |
| 2 | 843 | 0.74 | 0.79 | 99 | empty |
| 3 | 779 | 0.74 | 0.79 | 90 | empty |
| 4 | 346 | 0.71 | 0.83 | 30 | empty |
| 5 | 348 | 0.70 | 0.83 | 30 | empty |
Interfaces
12 interfaces between chains.
- A–B · 2287 Ų buried · 37 hydrogen bonds · protein-protein
- D–F · 2103 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 1548 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 1340 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1286 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 4L9Y · 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 4L9Y · PDBe 4L9Y · UniProt Q3J5L6
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