Research workbench
2.15 ångström resolution crystal structure of naphthoate synthase from salmonella typhimurium.
Analyse 2.15 ångström resolution crystal structure of naphthoate synthase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3H02
- Type
- protein
- Length
- 1,557 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Naphthoate synthase
- EC
- 4.1.3.36
- UniProt
- Q7CQ56
- Ligands
- BCT, SO4
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 6 distinct chains · 48% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Naphthoate synthase (EC 4.1.3.36) | protein | 266 | 48% helix, 18% strand | Q7CQ56 |
| B | Naphthoate synthase (EC 4.1.3.36) | protein | 262 | 45% helix, 17% strand | Q7CQ56 |
| C | Naphthoate synthase (EC 4.1.3.36) | protein | 262 | 50% helix, 16% strand | Q7CQ56 |
| D | Naphthoate synthase (EC 4.1.3.36) | protein | 264 | 49% helix, 18% strand | Q7CQ56 |
| E | Naphthoate synthase (EC 4.1.3.36) | protein | 264 | 48% helix, 18% strand | Q7CQ56 |
| F | Naphthoate synthase (EC 4.1.3.36) | protein | 239 | 47% helix, 20% strand | Q7CQ56 |
Ligands and binding sites
- BCT · Bicarbonate ion · ligand · 7 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 2 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 491 | 0.88 | 0.95 | 47 | empty |
| 2 | 659 | 0.79 | 0.84 | 57 | empty |
| 3 | 754 | 0.78 | 0.82 | 81 | empty |
| 4 | 514 | 0.71 | 0.81 | 50 | BCT |
| 5 | 585 | 0.71 | 0.79 | 63 | BCT |
Interfaces
12 interfaces between chains.
- A–D · 1858 Ų buried · 18 hydrogen bonds · protein-protein
- C–E · 1724 Ų buried · 22 hydrogen bonds · protein-protein
- B–F · 1698 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1677 Ų buried · 21 hydrogen bonds · protein-protein
- B–E · 1674 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 66 modified (engineered).
Compared structures
- 3H02 · 2.15 Angstrom Resolution Crystal Structure of Naphthoate Synthase from Salmonella… · the same entry in another collection · chain F against F, TM-score 1.00
- Q7CQ56 · AlphaFold monomer V2.0 prediction for 1,4-dihydroxy-2-naphthoyl-CoA synthase (Q7CQ56) · a predicted model of the same protein · chain F 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 Q7CQ56
- Elsewhere: RCSB PDB 3H02 · PDBe 3H02 · UniProt Q7CQ56
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