Research workbench
Structure of pseudomonas nrps protein, ambb-tc bound to ppant
Analyse Structure of pseudomonas nrps protein, ambb-tc bound to ppant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7X0F
- Type
- protein
- Length
- 1,803 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amb antimetabolite synthase ambb
- EC
- 6.2.1.67
- UniProt
- Q9I1H0
- Ligands
- PNS
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Amb antimetabolite synthase ambb (EC 6.2.1.67) | protein | 446 | 48% helix, 19% strand | Q9I1H0 |
| B | Amb antimetabolite synthase ambb (EC 6.2.1.67) | protein | 452 | 49% helix, 19% strand | Q9I1H0 |
| C | Amb antimetabolite synthase ambb (EC 6.2.1.67) | protein | 458 | 48% helix, 20% strand | Q9I1H0 |
| D | Amb antimetabolite synthase ambb (EC 6.2.1.67) | protein | 447 | 49% helix, 18% strand | Q9I1H0 |
Ligands and binding sites
- PNS · 4'-phosphopantetheine · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1004 | 0.85 | 0.86 | 80 | PNS |
| 2 | 1043 | 0.85 | 0.85 | 92 | PNS |
| 3 | 1112 | 0.84 | 0.85 | 83 | PNS |
| 4 | 1091 | 0.83 | 0.84 | 94 | PNS |
| 5 | 303 | 0.72 | 0.86 | 42 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1252 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1205 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 562 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 510 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 148 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (phosphopantetheinylation).
Compared structures
- 7X0F · Structure of Pseudomonas NRPS protein, AmbB-TC bound to Ppant · 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 Q9I1H0
- Elsewhere: RCSB PDB 7X0F · PDBe 7X0F · UniProt Q9I1H0
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