MolNFT v1 · #172727 · protein
Structure of the reversible pyrrole-2-carboxylic acid decarboxylase PA0254/HUDA
7ABN · Ubid-like decarboxylase: “Structure of the reversible pyrrole-2-carboxylic acid decarboxylase PA0254/HUDA”. X-ray diffraction, 3 ligands (4LU, MN, K), 16 pockets (best druggability 0.81). MolNFT v1 #172727 on GenesisL1: 3D…
- PDB
- 7ABN
- Type
- protein
- Length
- 1,980 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubid-like decarboxylase
- EC
- 4.1.1.-
- UniProt
- A0A5F1BUV8
- Ligands
- 4LU, MN, K
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, A | Ubid-like decarboxylase (EC 4.1.1.-) | protein | 496 | 34% helix, 25% strand | A0A5F1BUV8 |
| H, M | Ubid-like decarboxylase (EC 4.1.1.-) | protein | 494 | 34% helix, 24% strand | A0A5F1BUV8 |
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 · 4 copies · chains D, A, H, M
- MN · Manganese (II) ion · metal · 4 copies · chains D, A, H, M
- K · Potassium ion · metal · 4 copies · chains D, A, H, M
- IMD · Imidazole · additive · 4 copies · chains D, A, H, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 124 | 0.81 | 0.99 | 23 | empty |
| 2 | 121 | 0.81 | 0.99 | 24 | empty |
| 3 | 530 | 0.81 | 0.87 | 56 | K, 4LU, IMD |
| 4 | 490 | 0.81 | 0.87 | 57 | 4LU, IMD |
| 5 | 481 | 0.81 | 0.88 | 57 | IMD, 4LU |
Interfaces
6 interfaces between chains.
- A–H · 3683 Ų buried · 48 hydrogen bonds · protein-protein
- D–M · 3677 Ų buried · 49 hydrogen bonds · protein-protein
- D–A · 548 Ų buried · 5 hydrogen bonds · protein-protein
- D–H · 316 Ų buried · 1 hydrogen bond · protein-protein
- A–M · 308 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7ABN · Structure of the reversible pyrrole-2-carboxylic acid decarboxylase PA0254/HudA · the same entry in another collection · chain D against D, 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 A0A5F1BUV8
- Elsewhere: RCSB PDB 7ABN · PDBe 7ABN · UniProt A0A5F1BUV8
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