MolNFT v1 · #75799 · protein
Pantoate-beta-alanine ligase from yersinia pestis in complex with pantoate.
3Q12 · Pantoate--beta-alanine ligase: “Pantoate-beta-alanine ligase from yersinia pestis in complex with pantoate.”. X-ray diffraction, 2 ligands (PAF, CL), 16 pockets (best druggability 0.86). MolNFT v1 #75799 on GenesisL1: 3D structure…
- PDB
- 3Q12
- Type
- protein
- Length
- 1,137 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pantoate--beta-alanine ligase
- EC
- 6.3.2.1
- UniProt
- Q8ZBK7
- Ligands
- PAF, CL
- Pockets
- 16 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Pantoate--beta-alanine ligase (EC 6.3.2.1) | protein | 285 | 43% helix, 21% strand | Q8ZBK7 |
| B | Pantoate--beta-alanine ligase (EC 6.3.2.1) | protein | 284 | 42% helix, 21% strand | Q8ZBK7 |
| D | Pantoate--beta-alanine ligase (EC 6.3.2.1) | protein | 283 | 41% helix, 21% strand | Q8ZBK7 |
Ligands and binding sites
- PAF · Pantoate · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 364 | 0.86 | 0.95 | 65 | PAF, CL |
| 2 | 361 | 0.86 | 0.95 | 55 | PAF, CL |
| 3 | 1142 | 0.82 | 0.84 | 108 | empty |
| 4 | 754 | 0.79 | 0.83 | 60 | PAF |
| 5 | 682 | 0.78 | 0.82 | 62 | PAF |
Interfaces
6 interfaces between chains.
- A–B · 1270 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 1242 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 283 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 172 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 122 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3Q12 · Pantoate-beta-alanine ligase from Yersinia pestis in complex with pantoate. · the same entry in another collection · chain A against A, TM-score 1.00
- Q8ZBK7 · AlphaFold monomer V2.0 prediction for pantothenate synthetase (Q8ZBK7) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q8ZBK7
- Elsewhere: RCSB PDB 3Q12 · PDBe 3Q12 · UniProt Q8ZBK7
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