Research workbench
Structure of ATP-bound outward-facing TM287/288 in complex with sybody Sb_TM35
Analyse Structure of ATP-bound outward-facing TM287/288 in complex with sybody Sb_TM35 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QV0
- Type
- protein
- Length
- 2,529 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.12
- Source
- synthetic construct; Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 /…
- Molecule
- ABC transporter, ATP-binding protein; Uncharacterized ABC transporter ATP-binding protein…
- UniProt
- Q9WYC3, Q9WYC4
- Ligands
- ATP, MG
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · resolution 3.12 · 5 distinct chains · 61% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ABC transporter, ATP-binding protein | protein | 568 | 64% helix, 11% strand | Q9WYC3 |
| B | Uncharacterized ABC transporter ATP-binding protein TM_0288 | protein | 570 | 63% helix, 10% strand | Q9WYC4 |
| C | ABC transporter, ATP-binding protein | protein | 569 | 63% helix, 11% strand | Q9WYC3 |
| D | Uncharacterized ABC transporter ATP-binding protein TM_0288 | protein | 574 | 65% helix, 10% strand | Q9WYC4 |
| E, F | Sb_TM35 | protein | 124 | 2% helix, 48% strand | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 982 | 0.87 | 0.88 | 116 | ATP, MG |
| 2 | 1155 | 0.86 | 0.87 | 100 | ATP, MG |
| 3 | 718 | 0.81 | 0.85 | 82 | empty |
| 4 | 693 | 0.80 | 0.84 | 80 | empty |
| 5 | 190 | 0.74 | 0.90 | 33 | empty |
Interfaces
6 interfaces between chains.
- A–B · 7375 Ų buried · 71 hydrogen bonds · protein-protein
- C–D · 7311 Ų buried · 64 hydrogen bonds · protein-protein
- D–F · 595 Ų buried · 5 hydrogen bonds · protein-protein
- B–E · 534 Ų buried · 4 hydrogen bonds · protein-protein
- C–F · 400 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6QV0 · Structure of ATP-bound outward-facing TM287/288 in complex with sybody SB_TM35 · the same entry in another collection · chain F against F, TM-score 1.00
- Q9WYC4 · AlphaFold monomer V2.0 prediction for uncharacterized ABC transporter ATP-binding protein… · a predicted model of the same protein · chain B against A, TM-score 0.72
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 Q9WYC3
- Every structure of UniProt Q9WYC4
- Elsewhere: RCSB PDB 6QV0 · PDBe 6QV0 · UniProt Q9WYC3 · UniProt Q9WYC4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.