MolNFT v1 · #137258 · protein
Crystal structure of a pseudomonas malonate decarboxylase hetero- tetramer in complex with coenzyme a
5VJ1 · Mdca: “Crystal structure of a pseudomonas malonate decarboxylase hetero- tetramer in complex with coenzyme a”. X-ray diffraction, 2 ligands (COA, CL), 20 pockets (best druggability 0.83). MolNFT v1 #137258 on GenesisL1: 3D…
- PDB
- 5VJ1
- Type
- protein
- Length
- 2,368 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mdca; Mdcc; Mdcd; Mdce
- EC
- 2.1.3.10, 2.1.3.1
- UniProt
- Q9I6T0, Q4K4F7, A0A071KS24, A0A0C6EV56
- Ligands
- COA, CL
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, I | Mdca | protein | 548 | 35% helix, 18% strand | Q9I6T0 |
| C, K | Mdcc | protein | 97 | 26% helix, 36% strand | Q4K4F7 |
| D, L | Mdcd (EC 2.1.3.10, 2.1.3.1) | protein | 276 | 42% helix, 14% strand | A0A071KS24 |
| E, M | Mdce (EC 2.1.3.10) | protein | 263 | 46% helix, 18% strand | A0A0C6EV56 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 985 | 0.83 | 0.85 | 90 | empty |
| 2 | 1073 | 0.81 | 0.82 | 84 | empty |
| 3 | 59 | 0.71 | 0.98 | 22 | empty |
| 4 | 522 | 0.71 | 0.80 | 64 | empty |
| 5 | 416 | 0.70 | 0.81 | 49 | CL |
Interfaces
11 interfaces between chains.
- A–I · 4424 Ų buried · 76 hydrogen bonds · protein-protein
- L–M · 3672 Ų buried · 44 hydrogen bonds · protein-protein
- D–E · 3670 Ų buried · 48 hydrogen bonds · protein-protein
- I–K · 873 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 864 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5VJ1 · Crystal structure of a Pseudomonas malonate decarboxylase hetero-tetramer in complex with… · the same entry in another collection · chain M against M, TM-score 1.00
- Q4K4F7 · AlphaFold monomer V2.0 prediction for malonate decarboxylase acyl carrier protein (Q4K4F7) · a predicted model of the same protein · chain C 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 Q9I6T0
- Every structure of UniProt Q4K4F7
- Every structure of UniProt A0A071KS24
- Every structure of UniProt A0A0C6EV56
- Elsewhere: RCSB PDB 5VJ1 · PDBe 5VJ1 · UniProt Q9I6T0 · UniProt Q4K4F7 · UniProt A0A071KS24 · UniProt A0A0C6EV56
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