MolNFT v1 · #141261 · protein
Crystal structure of the complex of trimeric phosphopantetheine adenylyltransferase from acinetobacter baumannii with citrate ion at 1.87 a resolution
5Z1M: “Crystal structure of the complex of trimeric phosphopantetheine adenylyltransferase from acinetobacter…”. X-ray diffraction, 4 pockets (best druggability 0.78). MolNFT v1 #141261 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5Z1M
- Type
- protein
- Length
- 489 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphopantetheine adenylyltransferase
- EC
- 2.7.7.3
- UniProt
- A0A059ZFC5
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Phosphopantetheine adenylyltransferase (EC 2.7.7.3) | protein | 163 | 45% helix, 17% strand | A0A059ZFC5 |
Ligands and binding sites
- CIT · Citric acid · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 613 | 0.78 | 0.83 | 53 | CIT |
| 2 | 589 | 0.76 | 0.82 | 57 | CIT |
| 3 | 584 | 0.75 | 0.82 | 56 | CIT |
| 4 | 69 | 0.36 | 0.77 | 18 | empty |
Interfaces
3 interfaces between chains.
- B–C · 670 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 663 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 622 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5Z1M · Crystal structure of the complex of trimeric Phosphopantetheine adenylyltransferase from… · 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 A0A059ZFC5
- Elsewhere: RCSB PDB 5Z1M · PDBe 5Z1M · UniProt A0A059ZFC5
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