Research workbench
Structure of the enzyme-acp substrate gatekeeper complex required for biotin synthesis
Analyse Structure of the enzyme-acp substrate gatekeeper complex required for biotin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ETW
- Type
- protein
- Length
- 660 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pimelyl-[acyl-carrier protein] methyl ester esterase; Acyl carrier protein
- EC
- 3.1.1.85
- UniProt
- Q83PW0, Q0T5U2
- Ligands
- ZMK
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Pimelyl-[acyl-carrier protein] methyl ester esterase (EC 3.1.1.85) | protein | 255 | 46% helix, 17% strand | Q83PW0 |
| D, B | Acyl carrier protein | protein | 75 | 55% helix, 3% strand | Q0T5U2 |
Ligands and binding sites
- ZMK · methyl 7-{[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl]sulfanyl}-7-oxoheptanoate · ligand · 2 copies · chains C, D, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 979 | 0.74 | 0.77 | 75 | empty |
| 2 | 166 | 0.62 | 0.84 | 29 | ZMK |
| 3 | 170 | 0.62 | 0.83 | 27 | ZMK |
| 4 | 131 | 0.43 | 0.76 | 27 | empty |
| 5 | 113 | 0.41 | 0.76 | 18 | empty |
Interfaces
4 interfaces between chains.
- A–B · 611 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 593 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 530 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 61 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4ETW · Structure of the Enzyme-ACP Substrate Gatekeeper Complex Required for Biotin Synthesis · the same entry in another collection · chain B against B, TM-score 1.00
- Q83PW0 · AlphaFold monomer V2.0 prediction for pimeloyl-[acyl-carrier protein] methyl ester… · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q0T5U2 · AlphaFold monomer V2.0 prediction for acyl carrier protein (Q0T5U2) · a predicted model of the same protein · chain D against A, TM-score 0.96
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 Q83PW0
- Every structure of UniProt Q0T5U2
- Elsewhere: RCSB PDB 4ETW · PDBe 4ETW · UniProt Q83PW0 · UniProt Q0T5U2
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