MolNFT v1 · #141293 · protein
Crystal structure of bdca in complex with NADPH
5Z2L · Cyclic-di-gmp-binding biofilm dispersal mediator protein: “Crystal structure of bdca in complex with NADPH”. X-ray diffraction, 1 ligand (NDP), 20 pockets (best druggability 0.89). MolNFT v1 #141293 on GenesisL1: 3D structure…
- PDB
- 5Z2L
- Type
- protein
- Length
- 2,885 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclic-di-gmp-binding biofilm dispersal mediator protein
- UniProt
- P39333
- Ligands
- NDP
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 6 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, H, F, G, L | Cyclic-di-gmp-binding biofilm dispersal mediator protein | protein | 239 | 45% helix, 17% strand | P39333 |
| D | Cyclic-di-gmp-binding biofilm dispersal mediator protein | protein | 240 | 45% helix, 17% strand | P39333 |
| B | Cyclic-di-gmp-binding biofilm dispersal mediator protein | protein | 243 | 44% helix, 17% strand | P39333 |
| C, I | Cyclic-di-gmp-binding biofilm dispersal mediator protein | protein | 241 | 44% helix, 17% strand | P39333 |
| J | Cyclic-di-gmp-binding biofilm dispersal mediator protein | protein | 242 | 45% helix, 17% strand | P39333 |
| K | Cyclic-di-gmp-binding biofilm dispersal mediator protein | protein | 244 | 44% helix, 17% strand | P39333 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 12 copies · chains A, D, B, C, E, J, H, K, I, F, G, L
- EDO · 1,2-ethanediol · additive · 6 copies · chains D, B, C, E, I, G
- GOL · Glycerol · additive · 2 copies · chains C, E
- PG0 · 2-(2-methoxyethoxy)ethanol · additive · chains A, C
- PEG · Di(hydroxyethyl)ether · additive · chains K
- PG4 · Tetraethylene glycol · additive · chains H, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1137 | 0.89 | 0.90 | 158 | NDP, EDO |
| 2 | 1011 | 0.89 | 0.90 | 142 | GOL, NDP |
| 3 | 606 | 0.87 | 0.92 | 85 | empty |
| 4 | 710 | 0.78 | 0.82 | 75 | PG0, NDP |
| 5 | 592 | 0.77 | 0.83 | 62 | NDP |
Interfaces
21 interfaces between chains.
- E–F · 1731 Ų buried · 22 hydrogen bonds · protein-protein
- D–C · 1718 Ų buried · 24 hydrogen bonds · protein-protein
- J–I · 1717 Ų buried · 23 hydrogen bonds · protein-protein
- K–L · 1715 Ų buried · 24 hydrogen bonds · protein-protein
- H–G · 1713 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 5Z2L · Crystal structure of BdcA in complex with NADPH · the same entry in another collection · chain L against L, 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 P39333
- Elsewhere: RCSB PDB 5Z2L · PDBe 5Z2L · UniProt P39333
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.