Research workbench
High resolution structure of the pbp noct in complex with nopaline
Analyse High resolution structure of the pbp noct in complex with nopaline in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OVZ
- Type
- protein
- Length
- 515 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nopaline-binding periplasmic protein
- UniProt
- P35120
- Ligands
- 2W2, NA
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nopaline-binding periplasmic protein | protein | 259 | 39% helix, 22% strand | P35120 |
| B | Nopaline-binding periplasmic protein | protein | 256 | 40% helix, 23% strand | P35120 |
Ligands and binding sites
- 2W2 · N-[(1S)-4-carbamimidamido-1-carboxybutyl]-D-glutamic acid · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 7 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 778 | 0.71 | 0.77 | 55 | NA |
| 2 | 108 | 0.69 | 0.92 | 30 | 2W2 |
| 3 | 115 | 0.66 | 0.89 | 30 | 2W2 |
| 4 | 78 | 0.33 | 0.74 | 20 | empty |
| 5 | 61 | 0.29 | 0.74 | 16 | PEG |
Interfaces
1 interface between chains.
- A–B · 670 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5OVZ · High resolution structure of the PBP NocT in complex with nopaline · the same entry in another collection · chain B against B, TM-score 1.00
- P35120 · AlphaFold monomer V2.0 prediction for nopaline-binding periplasmic protein (P35120) · a predicted model of the same protein · chain B 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 P35120
- Elsewhere: RCSB PDB 5OVZ · PDBe 5OVZ · UniProt P35120
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