Research workbench
Cryo-EM structure of mycobacterium smegmatis arabinosyltransferase emba-embb-ACPM2 in complex with ethambutol
Analyse Cryo-EM structure of mycobacterium smegmatis arabinosyltransferase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BVC
- Type
- protein
- Length
- 2,231 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integral membrane indolylacetylinositol arabinosyltransferase emba; Integral membrane…
- EC
- 2.4.2.-, 2.4.2.34
- UniProt
- A0R613, I7GAQ2, A0R0B3
- Ligands
- CDL, F8L, PNS, 95E, CA, PO4
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 3 distinct chains · 34% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integral membrane indolylacetylinositol arabinosyltransferase emba (EC 2.4.2.-) | protein | 1078 | 33% helix, 11% strand | A0R613 |
| B | Integral membrane indolylacetylinositol arabinosyltransferase embb (EC 2.4.2.34) | protein | 1063 | 35% helix, 15% strand | I7GAQ2 |
| P | Meromycolate extension acyl carrier protein | protein | 90 | 46% helix, 2% strand | A0R0B3 |
Ligands and binding sites
- CDL · Cardiolipin · ligand · 2 copies · chains A, B
- F8L · [(2Z,6E,10E,14Z,18E,22Z,26Z)-3,7,11,15,19,23,27,31,35, 39-decamethyltetraconta-2,6,10,14,18,22,26,30,34,38-decaenyl] [(2S,3S,4S,5R)-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl] hydrogen phosphate · ligand · chains A
- PNS · 4'-phosphopantetheine · ligand · chains B, P
- 95E · Ethambutol · ligand · chains B
- CA · Calcium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1199 | 0.83 | 0.84 | 127 | PO4, 95E |
| 2 | 219 | 0.82 | 0.95 | 32 | empty |
| 3 | 507 | 0.81 | 0.88 | 40 | F8L |
| 4 | 509 | 0.76 | 0.83 | 41 | empty |
| 5 | 679 | 0.73 | 0.79 | 56 | empty |
Interfaces
2 interfaces between chains.
- A–B · 2308 Ų buried · 15 hydrogen bonds · protein-protein
- B–P · 852 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7BVC · Cryo-EM structure of Mycobacterium smegmatis arabinosyltransferase EmbA-EmbB-AcpM2 in… · 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 P against A, TM-score 0.81
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 A0R613
- Every structure of UniProt I7GAQ2
- Every structure of UniProt A0R0B3
- Elsewhere: RCSB PDB 7BVC · PDBe 7BVC · UniProt A0R613 · UniProt I7GAQ2 · UniProt A0R0B3
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