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Crystal structure of 4'-phosphopantetheinyl transferase acps from vibrio cholerae O1 biovar eltor
Analyse Crystal structure of 4'-phosphopantetheinyl transferase acps from vibrio… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QMN
- Type
- protein
- Length
- 3,024 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Holo-[acyl-carrier-protein] synthase
- EC
- 2.7.8.7
- UniProt
- Q9KPB6
- Ligands
- COA, A3P, CA, CL
- Pockets
- 20 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, F, G, H, I, J, K, L, M, N, P, Q, R, T, U, V | Holo-[acyl-carrier-protein] synthase (EC 2.7.8.7) | protein | 126 | 46% helix, 29% strand | Q9KPB6 |
| E, O | Holo-[acyl-carrier-protein] synthase (EC 2.7.8.7) | protein | 127 | 46% helix, 31% strand | Q9KPB6 |
| S, W | Holo-[acyl-carrier-protein] synthase (EC 2.7.8.7) | protein | 125 | 47% helix, 30% strand | Q9KPB6 |
| X | Holo-[acyl-carrier-protein] synthase (EC 2.7.8.7) | protein | 126 | 46% helix, 32% strand | Q9KPB6 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 24 copies · chains A, C, B, D, F, R, E, G, I, H, J, L, K, Q, M, N, O, P, S, U, T, V, W, X
- A3P · Adenosine-3'-5'-diphosphate · ligand · chains N, O
- CA · Calcium ion · metal · 46 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X
- CL · Chloride ion · ion · 9 copies · chains A, C, E, G, J, L, M, P, T
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 16 copies · chains A, B, C, E, G, H, I, M, O, P, Q, R, S, U, V, W
- ACT · Acetate ion · additive · 8 copies · chains A, C, E, J, K, R, S, T, W
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 6 copies · chains D, F, K, Q, L, N, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 565 | 0.67 | 0.77 | 58 | COA, CA |
| 2 | 530 | 0.66 | 0.77 | 55 | CA, MRD, COA |
| 3 | 508 | 0.66 | 0.77 | 56 | COA, CA, MRD |
| 4 | 284 | 0.53 | 0.75 | 47 | COA, CA, MPD |
| 5 | 237 | 0.51 | 0.76 | 47 | MPD, CA, COA, CL |
Interfaces
42 interfaces between chains.
- G–H · 905 Ų buried · 7 hydrogen bonds · protein-protein
- Q–R · 904 Ų buried · 11 hydrogen bonds · protein-protein
- P–Q · 892 Ų buried · 8 hydrogen bonds · protein-protein
- P–R · 883 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 882 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 modified (engineered).
Compared structures
- 3QMN · Crystal Structure of 4'-Phosphopantetheinyl Transferase AcpS from Vibrio cholerae O1… · the same entry in another collection · chain K against K, 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 Q9KPB6
- Elsewhere: RCSB PDB 3QMN · PDBe 3QMN · UniProt Q9KPB6
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