Research workbench
Crystal structure of malonyl-CoA decarboxylase from rhodopseudomonas palustris, northeast structural genomics consortium target RPR127
Analyse Crystal structure of malonyl-CoA decarboxylase from rhodopseudomonas palustris… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KSA
- Type
- protein
- Length
- 1,697 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malonyl-CoA decarboxylase
- EC
- 4.1.1.9
- UniProt
- Q6NCB2
- Ligands
- MG
- Pockets
- 17 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Malonyl-CoA decarboxylase (EC 4.1.1.9) | protein | 437 | 56% helix, 11% strand | Q6NCB2 |
| B | Malonyl-CoA decarboxylase (EC 4.1.1.9) | protein | 411 | 51% helix, 11% strand | Q6NCB2 |
| C | Malonyl-CoA decarboxylase (EC 4.1.1.9) | protein | 436 | 52% helix, 11% strand | Q6NCB2 |
| D | Malonyl-CoA decarboxylase (EC 4.1.1.9) | protein | 413 | 50% helix, 13% strand | Q6NCB2 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1016 | 0.79 | 0.81 | 107 | MG |
| 2 | 1179 | 0.77 | 0.80 | 104 | empty |
| 3 | 529 | 0.69 | 0.79 | 47 | empty |
| 4 | 480 | 0.67 | 0.79 | 45 | empty |
| 5 | 300 | 0.62 | 0.80 | 51 | MG |
Interfaces
6 interfaces between chains.
- C–D · 2395 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 2383 Ų buried · 39 hydrogen bonds · protein-protein
- A–D · 492 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 492 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 198 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 4KSA · Crystal Structure of Malonyl-CoA decarboxylase from Rhodopseudomonas palustris, Northeast… · 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 Q6NCB2
- Elsewhere: RCSB PDB 4KSA · PDBe 4KSA · UniProt Q6NCB2
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