MolNFT v1 · #169661 · protein
Pmtcd ABC exporter without the basket domain at C2 symmetry
6XJH · Phenol-soluble modulin export ABC transporter permease…: “Pmtcd ABC exporter without the basket domain at C2 symmetry”. Electron microscopy, 2 ligands (AGS, MG), 11 pockets (best druggability 0.70). MolNFT v1 #169661 on GenesisL1…
- PDB
- 6XJH
- Type
- protein
- Length
- 940 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phenol-soluble modulin export ABC transporter permease subunit pmtd; ABC transporter…
- UniProt
- A0A641A693, X5EJW5
- Ligands
- AGS, MG
- Pockets
- 11 · best druggability 0.70
Structure
electron microscopy · 2 distinct chains · 60% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phenol-soluble modulin export ABC transporter permease subunit pmtd | protein | 251 | 79% helix, 1% strand | A0A641A693 |
| C, D | ABC transporter ATP-binding protein | protein | 219 | 38% helix, 25% strand | X5EJW5 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 2 copies · chains C, D
- MG · Magnesium ion · metal · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 128 | 0.70 | 0.91 | 24 | empty |
| 2 | 235 | 0.70 | 0.86 | 42 | empty |
| 3 | 476 | 0.70 | 0.80 | 57 | AGS, MG |
| 4 | 379 | 0.70 | 0.81 | 55 | empty |
| 5 | 354 | 0.69 | 0.81 | 50 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1399 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1215 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 1204 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 1200 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6XJH · PmtCD ABC exporter without the basket domain at C2 symmetry · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A641A693
- Every structure of UniProt X5EJW5
- Elsewhere: RCSB PDB 6XJH · PDBe 6XJH · UniProt A0A641A693 · UniProt X5EJW5
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