Research workbench
Pseudomonas aeruginosa dapd (PA3666) in complex with L-2-aminopimelate
Analyse Pseudomonas aeruginosa dapd (PA3666) in complex with L-2-aminopimelate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3R5B
- Type
- protein
- Length
- 1,912 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tetrahydrodipicolinate N-succinyletransferase
- EC
- 2.3.1.117
- UniProt
- Q9Z9H2
- Ligands
- NPI
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Tetrahydrodipicolinate N-succinyletransferase (EC 2.3.1.117) | protein | 321 | 22% helix, 30% strand | Q9Z9H2 |
| B | Tetrahydrodipicolinate N-succinyletransferase (EC 2.3.1.117) | protein | 318 | 22% helix, 30% strand | Q9Z9H2 |
| C, F | Tetrahydrodipicolinate N-succinyletransferase (EC 2.3.1.117) | protein | 321 | 22% helix, 30% strand | Q9Z9H2 |
| E | Tetrahydrodipicolinate N-succinyletransferase (EC 2.3.1.117) | protein | 310 | 21% helix, 29% strand | Q9Z9H2 |
Ligands and binding sites
- NPI · (2S)-2-aminoheptanedioic acid · ligand · 5 copies · chains A, C, B, D, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 177 | 0.81 | 0.96 | 51 | empty |
| 2 | 184 | 0.80 | 0.95 | 51 | empty |
| 3 | 818 | 0.76 | 0.80 | 93 | NPI |
| 4 | 551 | 0.73 | 0.81 | 81 | NPI |
| 5 | 756 | 0.69 | 0.76 | 65 | NPI |
Interfaces
8 interfaces between chains.
- A–C · 1777 Ų buried · 34 hydrogen bonds · protein-protein
- D–F · 1750 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1742 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 1723 Ų buried · 29 hydrogen bonds · protein-protein
- D–E · 1673 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 3R5B · Pseudomonas aeruginosa DapD (PA3666) in complex with L-2-aminopimelate · 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 3R5B · PDBe 3R5B · UniProt Q9Z9H2
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