Research workbench
Crystal structure of apo matb from rhodopseudomonas palustris
Analyse Crystal structure of apo matb from rhodopseudomonas palustris in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FUQ
- Type
- protein
- Length
- 2,005 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malonyl CoA synthetase
- EC
- 6.2.1.-
- UniProt
- Q6ND88
- Ligands
- SO4
- Pockets
- 19 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Malonyl CoA synthetase (EC 6.2.1.-) | protein | 501 | 30% helix, 26% strand | Q6ND88 |
| C | Malonyl CoA synthetase (EC 6.2.1.-) | protein | 502 | 30% helix, 24% strand | Q6ND88 |
| D | Malonyl CoA synthetase (EC 6.2.1.-) | protein | 501 | 30% helix, 25% strand | Q6ND88 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, C, D
- GOL · Glycerol · additive · 21 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1033 | 0.81 | 0.82 | 95 | empty |
| 2 | 1109 | 0.75 | 0.78 | 96 | SO4, GOL |
| 3 | 724 | 0.75 | 0.80 | 89 | SO4, GOL |
| 4 | 956 | 0.73 | 0.77 | 97 | SO4, GOL |
| 5 | 410 | 0.73 | 0.83 | 52 | GOL |
Interfaces
3 interfaces between chains.
- B–D · 1142 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 1107 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 587 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 52 modified (engineered).
Compared structures
- 4FUQ · Crystal structure of apo MatB from Rhodopseudomonas palustris · 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 Q6ND88
- Elsewhere: RCSB PDB 4FUQ · PDBe 4FUQ · UniProt Q6ND88
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