Research workbench
Crystal structure of the L. plantarum acyl carrier protein synthase (ACPS)IN complex with D-alanyl carrier protein (DLTC1)
Analyse Crystal structure of the L. plantarum acyl carrier protein synthase (ACPS)IN… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7R49
- Type
- protein
- Length
- 591 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Holo-[acyl-carrier-protein] synthase; D-alanyl carrier protein 1
- EC
- 2.7.8.7
- UniProt
- Q88Z44, Q88VM8
- Ligands
- PNS
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Holo-[acyl-carrier-protein] synthase (EC 2.7.8.7) | protein | 119 | 40% helix, 31% strand | Q88Z44 |
| H | D-alanyl carrier protein 1 | protein | 77 | 60% helix, 0% strand | Q88VM8 |
| B | Holo-[acyl-carrier-protein] synthase (EC 2.7.8.7) | protein | 121 | 39% helix, 32% strand | Q88Z44 |
| E | D-alanyl carrier protein 1 | protein | 82 | 63% helix, 0% strand | Q88VM8 |
| F | D-alanyl carrier protein 1 | protein | 73 | 49% helix, 0% strand | Q88VM8 |
Ligands and binding sites
- PNS · 4'-phosphopantetheine · ligand · chains A, H, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 684 | 0.81 | 0.85 | 80 | empty |
| 2 | 618 | 0.80 | 0.86 | 73 | PNS |
| 3 | 666 | 0.78 | 0.83 | 74 | empty |
| 4 | 56 | 0.33 | 0.77 | 15 | empty |
| 5 | 69 | 0.33 | 0.75 | 19 | empty |
Interfaces
9 interfaces between chains.
- C–F · 763 Ų buried · 7 hydrogen bonds · protein-protein
- B–E · 758 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 752 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 740 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 739 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (phosphopantetheinylation).
Compared structures
- 7R49 · Crystal structure of the L. plantarum acyl carrier protein synthase (AcpS)in complex with… · the same entry in another collection · chain F against F, TM-score 1.00
- Q88Z44 · AlphaFold monomer V2.0 prediction for holo-[acyl-carrier-protein] synthase (Q88Z44) · a predicted model of the same protein · chain C against A, TM-score 0.98
- Q88VM8 · AlphaFold monomer V2.0 prediction for D-alanyl carrier protein 1 (Q88VM8) · a predicted model of the same protein · chain H against A, TM-score 0.94
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 Q88Z44
- Every structure of UniProt Q88VM8
- Elsewhere: RCSB PDB 7R49 · PDBe 7R49 · UniProt Q88Z44 · UniProt Q88VM8
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