MolNFT v1 · #146187 · protein
Crystal structure of the ttnd decarboxylase from the tautomycetin biosynthesis pathway of streptomyces griseochromogenes, apo form at 2.6 a resolution (P212121)
6DA6 · Ubid-like decarboxylase: “Crystal structure of the ttnd decarboxylase from the tautomycetin biosynthesis pathway of streptomyces…”. X-ray diffraction, 2 ligands (UNL, MG), 20 pockets (best druggability 0.81). MolNFT v1 #146187 on…
- PDB
- 6DA6
- Type
- protein
- Length
- 1,852 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubid-like decarboxylase
- EC
- 4.1.1.-
- UniProt
- C6ZCR8
- Ligands
- UNL, MG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ubid-like decarboxylase (EC 4.1.1.-) | protein | 464 | 32% helix, 23% strand | C6ZCR8 |
| C | Ubid-like decarboxylase (EC 4.1.1.-) | protein | 463 | 33% helix, 23% strand | C6ZCR8 |
| D | Ubid-like decarboxylase (EC 4.1.1.-) | protein | 461 | 33% helix, 23% strand | C6ZCR8 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 2 copies · chains A, C, B, D
- MG · Magnesium ion · metal · 3 copies · chains A, B, D
- GOL · Glycerol · additive · 16 copies · chains A, C, B, D
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 | 129 | 0.81 | 0.98 | 34 | UNL |
| 2 | 128 | 0.81 | 0.98 | 37 | UNL |
| 3 | 430 | 0.80 | 0.88 | 61 | GOL |
| 4 | 497 | 0.79 | 0.87 | 63 | GOL, MG |
| 5 | 363 | 0.77 | 0.87 | 52 | empty |
Interfaces
4 interfaces between chains.
- B–D · 3027 Ų buried · 47 hydrogen bonds · protein-protein
- A–C · 3007 Ų buried · 49 hydrogen bonds · protein-protein
- A–B · 858 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 848 Ų buried · 15 hydrogen bonds · protein-protein
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 C6ZCR8
- Elsewhere: RCSB PDB 6DA6 · PDBe 6DA6 · UniProt C6ZCR8
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