Research workbench
Heterodimeric ABC exporter tmrab in vanadate trapped outward-facing open conformation
Analyse Heterodimeric ABC exporter tmrab in vanadate trapped outward-facing open… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RAJ
- Type
- protein
- Length
- 1,282 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Multidrug resistance ABC transporter ATP-binding and permease protein; Nanobody NB9F10
- UniProt
- Q72J05, Q72J04
- Ligands
- AOV, ATP, MG
- Pockets
- 17 · best druggability 0.86
Structure
electron microscopy · 3 distinct chains · 52% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Multidrug resistance ABC transporter ATP-binding and permease protein | protein | 588 | 58% helix, 9% strand | Q72J05 |
| B | Multidrug resistance ABC transporter ATP-binding and permease protein | protein | 573 | 56% helix, 11% strand | Q72J04 |
| C | Nanobody NB9F10 | protein | 121 | 2% helix, 50% strand | — |
Ligands and binding sites
- AOV · Adp orthovanadate · ligand · chains A, B
- ATP · Adenosine-5'-triphosphate · ligand · 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
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 815 | 0.86 | 0.88 | 79 | empty |
| 2 | 761 | 0.84 | 0.87 | 65 | ATP, MG |
| 3 | 986 | 0.83 | 0.84 | 91 | AOV, MG |
| 4 | 200 | 0.72 | 0.88 | 25 | empty |
| 5 | 458 | 0.68 | 0.79 | 46 | empty |
Interfaces
2 interfaces between chains.
- A–B · 8055 Ų buried · 50 hydrogen bonds · protein-protein
- B–C · 686 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 6RAJ · Heterodimeric ABC exporter TmrAB in vanadate trapped outward-facing open conformation · the same entry in another collection · chain B against B, 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 Q72J05
- Every structure of UniProt Q72J04
- Elsewhere: RCSB PDB 6RAJ · PDBe 6RAJ · UniProt Q72J05 · UniProt Q72J04
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