Research workbench
Cryo-EM structure of mycobacterium smegmatis arabinosyltransferase EMBC2-ACPM2 in complex with ethambutol
Analyse Cryo-EM structure of mycobacterium smegmatis arabinosyltransferase EMBC2-ACPM2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BVE
- Type
- protein
- Length
- 2,236 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integral membrane indolylacetylinositol arabinosyltransferase embc; Meromycolate…
- EC
- 2.4.2.34
- UniProt
- I7FMU5, A0R0B3
- Ligands
- 95E, PN7, CA, PO4
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 2 distinct chains · 40% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Integral membrane indolylacetylinositol arabinosyltransferase embc (EC 2.4.2.34) | protein | 1034 | 39% helix, 14% strand | I7FMU5 |
| C, D | Meromycolate extension acyl carrier protein | protein | 84 | 54% helix, 2% strand | A0R0B3 |
Ligands and binding sites
- 95E · Ethambutol · ligand · 2 copies · chains A, B
- PN7 · N~3~-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy) butanoyl]-N-(2-sulfanylethyl)-beta-alaninamide · ligand · 2 copies · chains A, C, B, D
- CA · Calcium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 899 | 0.79 | 0.81 | 72 | PN7 |
| 2 | 918 | 0.79 | 0.81 | 76 | PN7 |
| 3 | 783 | 0.77 | 0.80 | 65 | PO4, 95E |
| 4 | 771 | 0.76 | 0.80 | 70 | PO4, 95E |
| 5 | 104 | 0.72 | 0.94 | 27 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1005 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 804 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 797 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
- 7BVE · Cryo-EM structure of Mycobacterium smegmatis arabinosyltransferase EmbC2-AcpM2 in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- A0R0B3 · AlphaFold monomer V2.0 prediction for meromycolate extension acyl carrier protein (A0R0B3) · a predicted model of the same protein · chain C against A, TM-score 0.85
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 I7FMU5
- Every structure of UniProt A0R0B3
- Elsewhere: RCSB PDB 7BVE · PDBe 7BVE · UniProt I7FMU5 · UniProt A0R0B3
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