Research workbench
Phosphopantetheine adenylyltransferase from mycobacterium tuberculosis in complex with 4'-phosphopantetheine
Analyse Phosphopantetheine adenylyltransferase from mycobacterium tuberculosis in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NBK
- Type
- protein
- Length
- 641 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphopantetheine adenylyltransferase
- EC
- 2.7.7.3
- UniProt
- P0A530
- Ligands
- PNS, NI
- Pockets
- 13 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phosphopantetheine adenylyltransferase (EC 2.7.7.3) | protein | 158 | 46% helix, 18% strand | P0A530 |
| C | Phosphopantetheine adenylyltransferase (EC 2.7.7.3) | protein | 162 | 43% helix, 18% strand | P0A530 |
| D | Phosphopantetheine adenylyltransferase (EC 2.7.7.3) | protein | 163 | 43% helix, 18% strand | P0A530 |
Ligands and binding sites
- PNS · 4'-phosphopantetheine · ligand · 4 copies · chains A, B, C, D
- NI · Nickel (II) ion · metal · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 431 | 0.67 | 0.79 | 50 | PNS |
| 2 | 378 | 0.67 | 0.80 | 39 | PNS |
| 3 | 396 | 0.66 | 0.79 | 44 | PNS |
| 4 | 366 | 0.65 | 0.80 | 41 | PNS |
| 5 | 299 | 0.62 | 0.80 | 34 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1426 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1035 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 495 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 162 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 28 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3NBK · Phosphopantetheine Adenylyltransferase from Mycobacterium tuberculosis in complex with… · 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 P0A530
- Elsewhere: RCSB PDB 3NBK · PDBe 3NBK · UniProt P0A530
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