MolNFT v1 · #190407 · protein
Structure of pseudomonas nrps protein, ambb-tc bound to ppant-L-ala
7X17 · Amb antimetabolite synthase ambb: “Structure of pseudomonas nrps protein, ambb-tc bound to ppant-L-ala”. X-ray diffraction, 1 ligand (868), 20 pockets (best druggability 0.84). MolNFT v1 #190407 on GenesisL1: 3D structure, binding…
- PDB
- 7X17
- Type
- protein
- Length
- 1,729 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
- 868
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Amb antimetabolite synthase ambb (EC 6.2.1.67) | protein | 410 | 46% helix, 20% strand | Q9I1H0 |
| B | Amb antimetabolite synthase ambb (EC 6.2.1.67) | protein | 421 | 49% helix, 20% strand | Q9I1H0 |
| C | Amb antimetabolite synthase ambb (EC 6.2.1.67) | protein | 455 | 47% helix, 20% strand | Q9I1H0 |
| D | Amb antimetabolite synthase ambb (EC 6.2.1.67) | protein | 443 | 48% helix, 19% strand | Q9I1H0 |
Ligands and binding sites
- 868 · S-[2-[3-[[(2S)-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] (2R)-2-azanylpropanethioate · 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 | 1091 | 0.84 | 0.85 | 97 | 868 |
| 2 | 1053 | 0.84 | 0.85 | 89 | 868 |
| 3 | 858 | 0.83 | 0.85 | 69 | 868 |
| 4 | 1137 | 0.83 | 0.83 | 85 | 868 |
| 5 | 718 | 0.71 | 0.78 | 67 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1363 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1252 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 537 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 523 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 141 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 7X17 · Structure of Pseudomonas NRPS protein, AmbB-TC bound to Ppant-L-Ala · 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 7X17 · PDBe 7X17 · UniProt Q9I1H0
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