Research workbench
Crystal structure of arabinosyltransferase EMBC2-ACPM2 complex from mycobacterium smegmatis complexed with di-arabinose
Analyse Crystal structure of arabinosyltransferase EMBC2-ACPM2 complex from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BVH
- Type
- protein
- Length
- 2,238 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integral membrane indolylacetylinositol arabinosyltransferase embc; Meromycolate…
- EC
- 2.4.2.34
- UniProt
- I7FMU5, A0R0B3
- Ligands
- BXY, BGC, GLC, CA, PO4
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Integral membrane indolylacetylinositol arabinosyltransferase embc (EC 2.4.2.34) | protein | 1035 | 41% helix, 16% strand | I7FMU5 |
| C, D | Meromycolate extension acyl carrier protein | protein | 84 | 60% helix, 2% strand | A0R0B3 |
Ligands and binding sites
- BXY · alpha-D-arabinofuranose · sugar · 8 copies · chains A, B
- BGC · beta-D-glucopyranose · sugar · 6 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · 6 copies · chains A, B
- 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 | 630 | 0.76 | 0.82 | 67 | BXY, BGC, GLC, PO4 |
| 2 | 460 | 0.75 | 0.84 | 42 | BXY, BGC, GLC, PO4 |
| 3 | 844 | 0.73 | 0.77 | 89 | BXY |
| 4 | 64 | 0.73 | 0.98 | 26 | empty |
| 5 | 70 | 0.72 | 0.97 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1072 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 995 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 937 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7BVH · Crystal structure of arabinosyltransferase EmbC2-AcpM2 complex from Mycobacterium… · 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 0.86
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 7BVH · PDBe 7BVH · UniProt I7FMU5 · UniProt A0R0B3
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