Research workbench
Dodecameric structure of the chlamydia trachomatis flavin prenyltransferase ubix ortholog CT220 with FMN and dmap
Analyse Dodecameric structure of the chlamydia trachomatis flavin prenyltransferase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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