Research workbench
Crystal structure of putative carboxynorspermidine decarboxylase protein from sinorhizobium meliloti
Analyse Crystal structure of putative carboxynorspermidine decarboxylase protein from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MT1
- Type
- protein
- Length
- 694 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative carboxynorspermidine decarboxylase protein
- EC
- 4.1.1.-
- UniProt
- Q92TG9
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative carboxynorspermidine decarboxylase protein (EC 4.1.1.-) | protein | 346 | 35% helix, 25% strand | Q92TG9 |
| B | Putative carboxynorspermidine decarboxylase protein (EC 4.1.1.-) | protein | 348 | 35% helix, 24% strand | Q92TG9 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 119 | 0.71 | 0.92 | 24 | empty |
| 2 | 468 | 0.67 | 0.79 | 58 | SO4 |
| 3 | 384 | 0.63 | 0.78 | 50 | SO4 |
| 4 | 124 | 0.52 | 0.81 | 28 | empty |
| 5 | 68 | 0.51 | 0.85 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 3076 Ų buried · 41 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 modified (engineered).
Compared structures
- 3MT1 · Crystal structure of putative carboxynorspermidine decarboxylase protein from… · the same entry in another collection · chain B against B, 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 Q92TG9
- Elsewhere: RCSB PDB 3MT1 · PDBe 3MT1 · UniProt Q92TG9
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