Research workbench
Crystal structure of the antibacterial peptide ABC transporter mcjd in an outward occluded state
Analyse Crystal structure of the antibacterial peptide ABC transporter mcjd in an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PL0
- 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
- ANP, BNG, MG
- Pockets
- 14 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 64% 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
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- BNG · nonyl beta-D-glucopyranoside · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 867 | 0.86 | 0.88 | 102 | BNG |
| 2 | 733 | 0.82 | 0.85 | 76 | empty |
| 3 | 291 | 0.81 | 0.92 | 35 | empty |
| 4 | 830 | 0.77 | 0.81 | 88 | ANP, MG |
| 5 | 503 | 0.77 | 0.85 | 55 | ANP, MG |
Interfaces
1 interface between chains.
- A–B · 7439 Ų buried · 79 hydrogen bonds · protein-protein
Compared structures
- 4PL0 · Crystal structure of the antibacterial peptide ABC transporter McjD in an 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 4PL0 · PDBe 4PL0 · UniProt Q9X2W0
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