Research workbench
M.TB mend with thdp and inhibitor bound
Analyse M.TB mend with thdp and inhibitor bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6O0J
- Type
- protein
- Length
- 2,119 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase
- EC
- 2.2.1.9
- UniProt
- P9WK11
- Ligands
- DNA, TPP, MG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase (EC 2.2.1.9) | protein | 527 | 38% helix, 20% strand | P9WK11 |
| D | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase (EC 2.2.1.9) | protein | 532 | 40% helix, 18% strand | P9WK11 |
| B | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase (EC 2.2.1.9) | protein | 524 | 38% helix, 19% strand | P9WK11 |
| C | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase (EC 2.2.1.9) | protein | 536 | 40% helix, 18% strand | P9WK11 |
Ligands and binding sites
- DNA · 1,4-dihydroxy-2-naphthoic acid · ligand · 4 copies · chains A, D, B, C
- TPP · Thiamine diphosphate · ligand · 2 copies · chains A, D, B, C
- MG · Magnesium ion · metal · 2 copies · chains D, C
- ACT · Acetate ion · additive · 3 copies · chains A, D, B, C
- FMT · Formic acid · additive · 3 copies · chains A, D, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 437 | 0.83 | 0.90 | 68 | FMT, MG, ACT, TPP |
| 2 | 460 | 0.83 | 0.90 | 79 | MG, ACT, TPP |
| 3 | 511 | 0.83 | 0.89 | 80 | DNA |
| 4 | 395 | 0.80 | 0.89 | 54 | DNA |
| 5 | 338 | 0.75 | 0.86 | 40 | empty |
Interfaces
6 interfaces between chains.
- A–D · 3248 Ų buried · 56 hydrogen bonds · protein-protein
- B–C · 3131 Ų buried · 55 hydrogen bonds · protein-protein
- A–C · 1547 Ų buried · 39 hydrogen bonds · protein-protein
- D–B · 1521 Ų buried · 39 hydrogen bonds · protein-protein
- D–C · 726 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
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 P9WK11
- Elsewhere: RCSB PDB 6O0J · PDBe 6O0J · UniProt P9WK11
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.