MolNFT v1 · #179993 · protein
Dodecameric structure of the chlamydia trachomatis flavin prenyltransferase ubix ortholog CT220 with FMN and dmap
7KM3: “Dodecameric structure of the chlamydia trachomatis flavin prenyltransferase ubix ortholog CT220 with FMN and…”. X-ray diffraction, 2 ligands (FMN, 4LR), 20 pockets (best druggability 0.84). MolNFT v1 #179993 on GenesisL1: 3D…
- PDB
- 7KM3
- Type
- protein
- Length
- 2,205 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Flavin prenyltransferase ubix
- EC
- 2.5.1.129
- UniProt
- O84222
- Ligands
- FMN, 4LR
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 9 distinct chains · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Flavin prenyltransferase ubix (EC 2.5.1.129) | protein | 175 | 47% helix, 18% strand | O84222 |
| I | Flavin prenyltransferase ubix (EC 2.5.1.129) | protein | 178 | 47% helix, 18% strand | O84222 |
| A | Flavin prenyltransferase ubix (EC 2.5.1.129) | protein | 183 | 48% helix, 17% strand | O84222 |
| B, H | Flavin prenyltransferase ubix (EC 2.5.1.129) | protein | 182 | 46% helix, 18% strand | O84222 |
| C, J | Flavin prenyltransferase ubix (EC 2.5.1.129) | protein | 187 | 47% helix, 17% strand | O84222 |
| D, K | Flavin prenyltransferase ubix (EC 2.5.1.129) | protein | 188 | 47% helix, 16% strand | O84222 |
| E | Flavin prenyltransferase ubix (EC 2.5.1.129) | protein | 182 | 46% helix, 17% strand | O84222 |
| F | Flavin prenyltransferase ubix (EC 2.5.1.129) | protein | 190 | 46% helix, 16% strand | O84222 |
| G | Flavin prenyltransferase ubix (EC 2.5.1.129) | protein | 183 | 45% helix, 17% strand | O84222 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 12 copies · chains L, C, D, I, A, B, E, K, J, F, G, H
- 4LR · Dimethylallyl monophosphate · ligand · 12 copies · chains I, D, H, A, B, E, G, K, L, C, F, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 750 | 0.84 | 0.87 | 106 | FMN, 4LR |
| 2 | 854 | 0.84 | 0.86 | 105 | FMN, 4LR |
| 3 | 615 | 0.84 | 0.88 | 76 | 4LR, FMN |
| 4 | 412 | 0.83 | 0.91 | 64 | 4LR, FMN |
| 5 | 338 | 0.82 | 0.92 | 53 | 4LR, FMN |
Interfaces
30 interfaces between chains.
- G–K · 1723 Ų buried · 18 hydrogen bonds · protein-protein
- F–J · 1673 Ų buried · 15 hydrogen bonds · protein-protein
- D–H · 1671 Ų buried · 17 hydrogen bonds · protein-protein
- I–B · 1656 Ų buried · 18 hydrogen bonds · protein-protein
- A–E · 1641 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 7KM3 · Dodecameric Structure of the Chlamydia trachomatis Flavin Prenyltransferase UbiX Ortholog… · the same entry in another collection · chain K against K, 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 O84222
- Elsewhere: RCSB PDB 7KM3 · PDBe 7KM3 · UniProt O84222
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