MolNFT v1 · #147420 · protein
Structure of the FAD binding protein MSMEG_5243 from mycobacterium smegmatis
6ECI · Pyridoxamine 5'-phosphate oxidase-related, FMN-binding…: “Structure of the FAD binding protein MSMEG_5243 from mycobacterium smegmatis”. X-ray diffraction, 2 ligands (FAD, CL), 20 pockets (best druggability 0.78). MolNFT v1 #147420…
- PDB
- 6ECI
- Type
- protein
- Length
- 2,423 residues
- Chains
- 20
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
- UniProt
- I7GF07
- Ligands
- FAD, CL
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 19 distinct chains · 17% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein | protein | 122 | 18% helix, 52% strand | I7GF07 |
| B, L | Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein | protein | 126 | 17% helix, 48% strand | I7GF07 |
| C | Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein | protein | 128 | 16% helix, 52% strand | I7GF07 |
| D | Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein | protein | 126 | 17% helix, 50% strand | I7GF07 |
| E | Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein | protein | 124 | 19% helix, 48% strand | I7GF07 |
| F | Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein | protein | 119 | 16% helix, 56% strand | I7GF07 |
| G | Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein | protein | 108 | 13% helix, 61% strand | I7GF07 |
| H | Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein | protein | 120 | 18% helix, 53% strand | I7GF07 |
| I | Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein | protein | 115 | 21% helix, 57% strand | I7GF07 |
| J | Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein | protein | 130 | 16% helix, 48% strand | I7GF07 |
| K | Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein | protein | 127 | 17% helix, 50% strand | I7GF07 |
| M | Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein | protein | 120 | 18% helix, 53% strand | I7GF07 |
| N | Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein | protein | 125 | 18% helix, 55% strand | I7GF07 |
| O | Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein | protein | 120 | 18% helix, 53% strand | I7GF07 |
| P | Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein | protein | 132 | 15% helix, 49% strand | I7GF07 |
| Q | Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein | protein | 116 | 18% helix, 53% strand | I7GF07 |
| R | Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein | protein | 109 | 7% helix, 60% strand | I7GF07 |
| S | Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein | protein | 117 | 18% helix, 48% strand | I7GF07 |
| T | Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein | protein | 113 | 19% helix, 51% strand | I7GF07 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 17 copies · chains A, B, C, D, H, E, F, G, I, J, K, L, M, N, O, P, Q, R, S, T
- CL · Chloride ion · ion · chains A, D, E, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 654 | 0.78 | 0.83 | 89 | empty |
| 2 | 753 | 0.77 | 0.82 | 85 | FAD |
| 3 | 969 | 0.77 | 0.80 | 78 | FAD |
| 4 | 476 | 0.74 | 0.83 | 42 | empty |
| 5 | 1148 | 0.72 | 0.76 | 72 | empty |
Interfaces
35 interfaces between chains.
- K–L · 1404 Ų buried · 22 hydrogen bonds · protein-protein
- O–P · 1372 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1274 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1222 Ų buried · 22 hydrogen bonds · protein-protein
- I–J · 1185 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 6ECI · Structure of the FAD binding protein MSMEG_5243 from Mycobacterium smegmatis · 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 I7GF07
- Elsewhere: RCSB PDB 6ECI · PDBe 6ECI · UniProt I7GF07
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