MolNFT v1 · #90546 · protein
Synechocystis sp. pcc 6803 1,4-dihydroxy-2-naphthoyl-coenzyme a synthase (menb) in complex with bicarbonate
4EML · Naphthoate synthase: “Synechocystis sp. pcc 6803 1,4-dihydroxy-2-naphthoyl-coenzyme a synthase (menb) in complex with bicarbonate”. X-ray diffraction, 3 ligands (BCT, CL, SO4), 12 pockets (best druggability 0.88). MolNFT v1 #90546…
- PDB
- 4EML
- Type
- protein
- Length
- 1,555 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Naphthoate synthase
- EC
- 4.1.3.36
- UniProt
- P73495
- Ligands
- BCT, CL, SO4
- Pockets
- 12 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Naphthoate synthase (EC 4.1.3.36) | protein | 261 | 48% helix, 19% strand | P73495 |
| B, C | Naphthoate synthase (EC 4.1.3.36) | protein | 259 | 48% helix, 18% strand | P73495 |
| D | Naphthoate synthase (EC 4.1.3.36) | protein | 258 | 48% helix, 19% strand | P73495 |
| E, F | Naphthoate synthase (EC 4.1.3.36) | protein | 259 | 48% helix, 19% strand | P73495 |
Ligands and binding sites
- BCT · Bicarbonate ion · ligand · 6 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 3 copies · chains A, D, B, E, F
- SO4 · Sulfate ion · ion · chains C, E
- GOL · Glycerol · additive · 7 copies · chains B, C, E, D, A, F
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains A, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 504 | 0.88 | 0.95 | 48 | empty |
| 2 | 964 | 0.86 | 0.87 | 116 | BCT |
| 3 | 1028 | 0.84 | 0.85 | 115 | BCT |
| 4 | 1086 | 0.84 | 0.85 | 112 | BCT, GOL, SO4 |
| 5 | 404 | 0.73 | 0.84 | 57 | CL |
Interfaces
12 interfaces between chains.
- B–C · 1833 Ų buried · 25 hydrogen bonds · protein-protein
- A–F · 1797 Ų buried · 34 hydrogen bonds · protein-protein
- A–E · 1779 Ų buried · 24 hydrogen bonds · protein-protein
- D–F · 1772 Ų buried · 23 hydrogen bonds · protein-protein
- C–E · 1744 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 4EML · Synechocystis sp. PCC 6803 1,4-dihydroxy-2-naphthoyl-coenzyme A synthase (MenB) in… · 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 P73495
- Elsewhere: RCSB PDB 4EML · PDBe 4EML · UniProt P73495
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