Research workbench
Crystal structure of pseudomonas malonate decarboxylase mdcd-mdce hetero-dimer
Analyse Crystal structure of pseudomonas malonate decarboxylase mdcd-mdce hetero-dimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VIP
- Type
- protein
- Length
- 1,009 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mdce; Mdcd
- EC
- 2.1.3.10, 2.1.3.1
- UniProt
- A0A0C6EV56, A0A071KS24
- Pockets
- 7 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mdce (EC 2.1.3.10) | protein | 255 | 43% helix, 18% strand | A0A0C6EV56 |
| B | Mdcd (EC 2.1.3.10, 2.1.3.1) | protein | 228 | 45% helix, 20% strand | A0A071KS24 |
| C | Mdce (EC 2.1.3.10) | protein | 254 | 43% helix, 19% strand | A0A0C6EV56 |
| D | Mdcd (EC 2.1.3.10, 2.1.3.1) | protein | 272 | 44% helix, 16% strand | A0A071KS24 |
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 570 | 0.70 | 0.79 | 73 | empty |
| 2 | 417 | 0.66 | 0.79 | 59 | empty |
| 3 | 372 | 0.61 | 0.77 | 50 | empty |
| 4 | 228 | 0.52 | 0.77 | 42 | empty |
| 5 | 168 | 0.52 | 0.79 | 24 | empty |
Interfaces
3 interfaces between chains.
- C–D · 3357 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 2979 Ų buried · 37 hydrogen bonds · protein-protein
- B–D · 752 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 5VIP · Crystal structure of Pseudomonas malonate decarboxylase MdcD-MdcE hetero-dimer · 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 A0A0C6EV56
- Every structure of UniProt A0A071KS24
- Elsewhere: RCSB PDB 5VIP · PDBe 5VIP · UniProt A0A0C6EV56 · UniProt A0A071KS24
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.