MolNFT v1 · #158639 · protein
M.TB mend intii bound with inhibitor
6O04 · 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1…: “M.TB mend intii bound with inhibitor”. X-ray diffraction, 4 ligands (DNA, TOI, MG), 20 pockets (best druggability 0.85). MolNFT v1 #158639 on GenesisL1: 3D structure, binding…
- PDB
- 6O04
- Type
- protein
- Length
- 2,144 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, TOI, MG, CL
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 18% 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 | 532 | 39% helix, 19% strand | P9WK11 |
| D | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase (EC 2.2.1.9) | protein | 542 | 40% helix, 18% strand | P9WK11 |
| B | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase (EC 2.2.1.9) | protein | 532 | 39% helix, 19% strand | P9WK11 |
| C | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase (EC 2.2.1.9) | protein | 538 | 40% helix, 17% strand | P9WK11 |
Ligands and binding sites
- DNA · 1,4-dihydroxy-2-naphthoic acid · ligand · 4 copies · chains A, D, B, C
- TOI · (1~{R},2~{S},5~{S},6~{S})-2-[(1~{S})-1-[3-[(4-azanylidene-2-methyl-1~{H}-pyrimidin-5-yl)methyl]-4-methyl-5-[2-[oxidanyl (phosphonooxy)phosphoryl]oxyethyl]-1,3-thiazol-3-ium-2-yl]-1,4-bis(oxidanyl)-4-oxidanylidene-butyl]-6-oxidanyl-5-(3-oxid anyl-3-oxidanylidene-prop-1-en-2-yl)oxy-cyclohex-3-ene-1-carboxylic acid · ligand · 2 copies · chains A, D, B, C
- MG · Magnesium ion · metal · 2 copies · chains D, C
- CL · Chloride ion · ion · chains B
- ACT · Acetate ion · additive · 2 copies · chains A, B, D
- FMT · Formic acid · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 879 | 0.85 | 0.87 | 103 | DNA, ACT |
| 2 | 615 | 0.84 | 0.89 | 90 | DNA |
| 3 | 505 | 0.83 | 0.90 | 76 | MG, TOI |
| 4 | 303 | 0.81 | 0.92 | 64 | TOI |
| 5 | 243 | 0.71 | 0.86 | 34 | empty |
Interfaces
6 interfaces between chains.
- A–D · 3319 Ų buried · 51 hydrogen bonds · protein-protein
- B–C · 3175 Ų buried · 52 hydrogen bonds · protein-protein
- D–B · 1563 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 1542 Ų buried · 42 hydrogen bonds · protein-protein
- D–C · 724 Ų buried · 7 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 6O04 · PDBe 6O04 · UniProt P9WK11
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