MolNFT v1 · #77123 · protein
Pseudomonas aeruginosa dapd (PA3666) in complex with CoA and succinate
3R5C · Tetrahydrodipicolinate N-succinyletransferase: “Pseudomonas aeruginosa dapd (PA3666) in complex with CoA and succinate”. X-ray diffraction, 1 ligand (COA), 11 pockets (best druggability 0.79). MolNFT v1 #77123 on GenesisL1: 3D…
- PDB
- 3R5C
- Type
- protein
- Length
- 1,010 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tetrahydrodipicolinate N-succinyletransferase
- EC
- 2.3.1.117
- UniProt
- Q9Z9H2
- Ligands
- COA
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 23% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tetrahydrodipicolinate N-succinyletransferase (EC 2.3.1.117) | protein | 338 | 24% helix, 30% strand | Q9Z9H2 |
| B | Tetrahydrodipicolinate N-succinyletransferase (EC 2.3.1.117) | protein | 337 | 23% helix, 29% strand | Q9Z9H2 |
| C | Tetrahydrodipicolinate N-succinyletransferase (EC 2.3.1.117) | protein | 335 | 23% helix, 29% strand | Q9Z9H2 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 3 copies · chains A, C, B
- SIN · Succinic acid · additive · 3 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 145 | 0.79 | 0.96 | 47 | empty |
| 2 | 414 | 0.61 | 0.76 | 57 | COA, SIN |
| 3 | 342 | 0.59 | 0.77 | 56 | COA, SIN |
| 4 | 329 | 0.58 | 0.76 | 54 | SIN, COA |
| 5 | 175 | 0.47 | 0.75 | 30 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1751 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 1744 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 1730 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 3R5C · Pseudomonas aeruginosa DapD (PA3666) in complex with CoA and succinate · 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 Q9Z9H2
- Elsewhere: RCSB PDB 3R5C · PDBe 3R5C · UniProt Q9Z9H2
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