Research workbench
Cryo-EM structure of mycobacterium tuberculosis arabinosyltransferase emba-embb-ACPM2 in complex with ethambutol
Analyse Cryo-EM structure of mycobacterium tuberculosis arabinosyltransferase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BVF
- Type
- protein
- Length
- 2,221 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable arabinosyltransferase B; Probable arabinosyltransferase a; Meromycolate…
- EC
- 2.4.2.-
- UniProt
- P9WNL7, P9WNL9, A0R0B3
- Ligands
- CDL, 95E, DSL, CA
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 3 distinct chains · 35% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Probable arabinosyltransferase B (EC 2.4.2.-) | protein | 1054 | 35% helix, 12% strand | P9WNL7 |
| A | Probable arabinosyltransferase a (EC 2.4.2.-) | protein | 1087 | 35% helix, 14% strand | P9WNL9 |
| P | Meromycolate extension acyl carrier protein | protein | 80 | 46% helix, 3% strand | A0R0B3 |
Ligands and binding sites
- CDL · Cardiolipin · ligand · 2 copies · chains B, A
- 95E · Ethambutol · ligand · chains B
- DSL · Mono-trans, octa-cis decaprenyl-phosphate · ligand · chains B
- CA · Calcium ion · metal · 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 473 | 0.82 | 0.89 | 38 | empty |
| 2 | 1183 | 0.82 | 0.83 | 131 | 95E, DSL |
| 3 | 1052 | 0.79 | 0.80 | 93 | CDL |
| 4 | 314 | 0.75 | 0.87 | 48 | empty |
| 5 | 584 | 0.69 | 0.78 | 48 | empty |
Interfaces
2 interfaces between chains.
- B–A · 2136 Ų buried · 13 hydrogen bonds · protein-protein
- A–P · 1308 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 7BVF · Cryo-EM structure of Mycobacterium tuberculosis arabinosyltransferase EmbA-EmbB-AcpM2 in… · the same entry in another collection · chain B against B, TM-score 1.00
- P9WNL9 · AlphaFold monomer V2.0 prediction for probable arabinosyltransferase a (P9WNL9) · a predicted model of the same protein · chain A against A, TM-score 1.00
- P9WNL7 · AlphaFold monomer V2.0 prediction for probable arabinosyltransferase B (P9WNL7) · a predicted model of the same protein · chain B against A, TM-score 0.99
- 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 0.87
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 P9WNL7
- Every structure of UniProt P9WNL9
- Every structure of UniProt A0R0B3
- Elsewhere: RCSB PDB 7BVF · PDBe 7BVF · UniProt P9WNL7 · UniProt P9WNL9 · UniProt A0R0B3
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