MolNFT v1 · #185056 · protein
Crystal structure of phenazine 1-carboxylic acid decarboxylase from mycobacterium fortuitum
7PDA · Ubid family decarboxylase: “Crystal structure of phenazine 1-carboxylic acid decarboxylase from mycobacterium fortuitum”. X-ray diffraction, 3 ligands (4LU, MN, NA), 5 pockets (best druggability 0.80). MolNFT v1 #185056 on…
- PDB
- 7PDA
- Type
- protein
- Length
- 482 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubid family decarboxylase; Unk
- UniProt
- A0A0N9Y7U2
- Ligands
- 4LU, MN, NA
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubid family decarboxylase | protein | 477 | 29% helix, 23% strand | A0A0N9Y7U2 |
| B | Unk | protein | 5 | 0% helix, 40% strand | — |
Ligands and binding sites
- 4LU · 1-deoxy-5-O-phosphono-1-(3,3,4,5-tetramethyl-9,11-dioxo-2,3,8,9,10,11-hexahydro-7H-quinolino[1,8-fg]pteridin-12-ium-7-yl)-D-ribitol · ligand · chains A
- MN · Manganese (II) ion · metal · chains A
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1051 | 0.80 | 0.81 | 74 | 4LU, NA |
| 2 | 152 | 0.49 | 0.77 | 17 | empty |
| 3 | 158 | 0.46 | 0.76 | 28 | empty |
| 4 | 79 | 0.35 | 0.76 | 19 | empty |
| 5 | 59 | 0.28 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 207 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7PDA · Crystal structure of Phenazine 1-carboxylic acid decarboxylase from Mycobacterium… · 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 A0A0N9Y7U2
- Elsewhere: RCSB PDB 7PDA · PDBe 7PDA · UniProt A0A0N9Y7U2
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