Research workbench
Mycobacterium smegmatis arabinosyltransferase complex EMBB2-ACPM2 in substrate dpa bound asymmetric "active state"
Analyse Mycobacterium smegmatis arabinosyltransferase complex EMBB2-ACPM2 in substrate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BWR
- Type
- protein
- Length
- 2,064 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integral membrane indolylacetylinositol arabinosyltransferase embb; Meromycolate…
- EC
- 2.4.2.34
- UniProt
- I7GAQ2, A0R0B3
- Ligands
- F8L, CA
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 3 distinct chains · 32% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integral membrane indolylacetylinositol arabinosyltransferase embb (EC 2.4.2.34) | protein | 1058 | 31% helix, 15% strand | I7GAQ2 |
| B | Integral membrane indolylacetylinositol arabinosyltransferase embb (EC 2.4.2.34) | protein | 850 | 31% helix, 10% strand | I7GAQ2 |
| C, D | Meromycolate extension acyl carrier protein | protein | 78 | 50% helix, 0% strand | A0R0B3 |
Ligands and binding sites
- 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, B
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 831 | 0.81 | 0.84 | 125 | empty |
| 2 | 519 | 0.79 | 0.86 | 70 | empty |
| 3 | 876 | 0.78 | 0.81 | 76 | empty |
| 4 | 540 | 0.76 | 0.83 | 64 | empty |
| 5 | 678 | 0.76 | 0.81 | 70 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1373 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 819 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 694 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7BWR · Mycobacterium smegmatis arabinosyltransferase complex EmbB2-AcpM2 in substrate DPA bound… · 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 D 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 I7GAQ2
- Every structure of UniProt A0R0B3
- Elsewhere: RCSB PDB 7BWR · PDBe 7BWR · UniProt I7GAQ2 · UniProt A0R0B3
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