MolNFT v1 · #126906 · protein
Crystal structure of pseudomonas stutzeri flavinyl transferase apbe, apo form
5MGY · FAD:PROTEIN FMN transferase: “Crystal structure of pseudomonas stutzeri flavinyl transferase apbe, apo form”. X-ray diffraction, 1 ligand (MG), 19 pockets (best druggability 0.82). MolNFT v1 #126906 on GenesisL1: 3D structure…
- PDB
- 5MGY
- Type
- protein
- Length
- 2,473 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FAD:PROTEIN FMN transferase
- EC
- 2.7.1.180
- UniProt
- A0A2N8RKH1
- Ligands
- MG
- Pockets
- 19 · best druggability 0.82
Structure
x-ray diffraction · 7 distinct chains · 34% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, E | FAD:PROTEIN FMN transferase (EC 2.7.1.180) | protein | 316 | 34% helix, 28% strand | A0A2N8RKH1 |
| B | FAD:PROTEIN FMN transferase (EC 2.7.1.180) | protein | 303 | 34% helix, 27% strand | A0A2N8RKH1 |
| G | FAD:PROTEIN FMN transferase (EC 2.7.1.180) | protein | 299 | 36% helix, 25% strand | A0A2N8RKH1 |
| A | FAD:PROTEIN FMN transferase (EC 2.7.1.180) | protein | 305 | 34% helix, 29% strand | A0A2N8RKH1 |
| C | FAD:PROTEIN FMN transferase (EC 2.7.1.180) | protein | 310 | 34% helix, 26% strand | A0A2N8RKH1 |
| D | FAD:PROTEIN FMN transferase (EC 2.7.1.180) | protein | 309 | 34% helix, 26% strand | A0A2N8RKH1 |
| F | FAD:PROTEIN FMN transferase (EC 2.7.1.180) | protein | 315 | 35% helix, 27% strand | A0A2N8RKH1 |
Ligands and binding sites
- MG · Magnesium ion · metal · 8 copies · chains H, B, G, A, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 710 | 0.82 | 0.86 | 83 | MG |
| 2 | 742 | 0.82 | 0.86 | 85 | empty |
| 3 | 735 | 0.82 | 0.86 | 80 | MG |
| 4 | 780 | 0.82 | 0.85 | 87 | empty |
| 5 | 854 | 0.82 | 0.84 | 85 | MG |
Interfaces
9 interfaces between chains.
- G–F · 1001 Ų buried · 7 hydrogen bonds · protein-protein
- H–E · 995 Ų buried · 11 hydrogen bonds · protein-protein
- H–F · 972 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 931 Ų buried · 7 hydrogen bonds · protein-protein
- G–E · 865 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5MGY · Crystal structure of Pseudomonas stutzeri flavinyl transferase ApbE, apo form · the same entry in another collection · chain H against H, 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 A0A2N8RKH1
- Elsewhere: RCSB PDB 5MGY · PDBe 5MGY · UniProt A0A2N8RKH1
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