MolNFT v1 · #137251 · protein
Crystal structure of a pseudomonas malonate decarboxylase hetero- tetramer in complex with malonate
5VIT · Mdca: “Crystal structure of a pseudomonas malonate decarboxylase hetero- tetramer in complex with malonate”. X-ray diffraction, 20 pockets (best druggability 0.81). MolNFT v1 #137251 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5VIT
- Type
- protein
- Length
- 4,708 residues
- Chains
- 16
- 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
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, P, I, V | Mdca | protein | 548 | 36% helix, 18% strand | Q9I6T0 |
| C, R, K, X | Mdcc | protein | 97 | 27% helix, 39% strand | Q4K4F7 |
| D, S, L, Y | Mdcd (EC 2.1.3.10, 2.1.3.1) | protein | 276 | 45% helix, 16% strand | A0A071KS24 |
| E, T, M, Z | Mdce (EC 2.1.3.10) | protein | 256 | 43% helix, 18% strand | A0A0C6EV56 |
Ligands and binding sites
- MLI · Malonate ion · additive · 4 copies · chains A, P, I, V
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1089 | 0.81 | 0.82 | 90 | empty |
| 2 | 1079 | 0.81 | 0.82 | 90 | empty |
| 3 | 1102 | 0.80 | 0.82 | 90 | empty |
| 4 | 1092 | 0.80 | 0.81 | 87 | empty |
| 5 | 86 | 0.78 | 0.99 | 21 | empty |
Interfaces
24 interfaces between chains.
- A–P · 4432 Ų buried · 86 hydrogen bonds · protein-protein
- I–V · 4399 Ų buried · 83 hydrogen bonds · protein-protein
- D–E · 3439 Ų buried · 40 hydrogen bonds · protein-protein
- Y–Z · 3416 Ų buried · 40 hydrogen bonds · protein-protein
- S–T · 3410 Ų buried · 44 hydrogen bonds · protein-protein
Compared structures
- 5VIT · Crystal structure of a Pseudomonas malonate decarboxylase hetero-tetramer in complex with… · the same entry in another collection · chain Z against Z, 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 Q9I6T0
- Every structure of UniProt Q4K4F7
- Every structure of UniProt A0A071KS24
- Every structure of UniProt A0A0C6EV56
- Elsewhere: RCSB PDB 5VIT · PDBe 5VIT · UniProt Q9I6T0 · UniProt Q4K4F7 · UniProt A0A071KS24 · UniProt A0A0C6EV56
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