Research workbench
Structure of the antibacterial peptide ABC transporter mcjd in a high energy outward occluded intermediate state
Analyse Structure of the antibacterial peptide ABC transporter mcjd in a high energy… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OFR
- Type
- protein
- Length
- 1,147 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Microcin-J25 export ATP-BINDING/PERMEASE protein mcjd
- UniProt
- Q9X2W0
- Ligands
- ADP, MG, VO4
- Pockets
- 19 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 63% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Microcin-J25 export ATP-BINDING/PERMEASE protein mcjd | protein | 571 | 63% helix, 11% strand | Q9X2W0 |
| B | Microcin-J25 export ATP-BINDING/PERMEASE protein mcjd | protein | 576 | 64% helix, 10% strand | Q9X2W0 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- VO4 · Vanadate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 396 | 0.81 | 0.89 | 43 | empty |
| 2 | 513 | 0.80 | 0.87 | 57 | empty |
| 3 | 287 | 0.80 | 0.92 | 28 | empty |
| 4 | 498 | 0.80 | 0.86 | 61 | empty |
| 5 | 534 | 0.78 | 0.85 | 63 | ADP, MG, VO4 |
Interfaces
1 interface between chains.
- A–B · 7480 Ų buried · 77 hydrogen bonds · protein-protein
Compared structures
- 5OFR · Structure of the antibacterial peptide ABC transporter McjD in a high energy outward… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9X2W0 · AlphaFold monomer V2.0 prediction for microcin-J25 export ATP- BINDING/PERMEASE protein… · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q9X2W0
- Elsewhere: RCSB PDB 5OFR · PDBe 5OFR · UniProt Q9X2W0
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