MolNFT v1 · #105283 · protein
Crystal structure of the alcanivorax borkumensis ydah transporter reveals an unusual topology
4R0C · Abgt putative transporter family: “Crystal structure of the alcanivorax borkumensis ydah transporter reveals an unusual topology”. X-ray diffraction, 1 ligand (NA), 20 pockets (best druggability 0.76). MolNFT v1 #105283 on…
- PDB
- 4R0C
- Type
- protein
- Length
- 1,901 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Abgt putative transporter family
- UniProt
- Q0VR69
- Ligands
- NA
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 71% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Abgt putative transporter family | protein | 476 | 70% helix, 0% strand | Q0VR69 |
| B | Abgt putative transporter family | protein | 468 | 71% helix, 1% strand | Q0VR69 |
| C | Abgt putative transporter family | protein | 474 | 72% helix, 1% strand | Q0VR69 |
| D | Abgt putative transporter family | protein | 483 | 70% helix, 1% strand | Q0VR69 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- LMT · Dodecyl-beta-D-maltoside · additive · 6 copies · chains A, B, C, D
- BOG · octyl beta-D-glucopyranoside · additive · 4 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 868 | 0.76 | 0.79 | 71 | empty |
| 2 | 823 | 0.76 | 0.79 | 68 | LMT |
| 3 | 770 | 0.76 | 0.80 | 67 | empty |
| 4 | 806 | 0.75 | 0.79 | 67 | LMT, BOG |
| 5 | 647 | 0.74 | 0.80 | 54 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1770 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 1770 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 1117 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4R0C · Crystal structure of the Alcanivorax borkumensis YdaH transporter reveals an unusual… · the same entry in another collection · chain D against D, 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 Q0VR69
- Elsewhere: RCSB PDB 4R0C · PDBe 4R0C · UniProt Q0VR69
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