Research workbench
Structure of atpgs-bound outward-facing TM287/288 in complex with sybody SB_TM35
Analyse Structure of atpgs-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
- 6QUZ
- Type
- protein
- Length
- 2,529 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ABC transporter, ATP-binding protein; Uncharacterized ABC transporter ATP-binding protein…
- UniProt
- Q9WYC3, Q9WYC4
- Ligands
- AGS, MG
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 5 distinct chains · 61% helix, 13% 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 | 64% 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 | 64% helix, 10% strand | Q9WYC4 |
| E, F | SB_TM35 | protein | 124 | 2% helix, 47% strand | — |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1178 | 0.88 | 0.89 | 125 | AGS, MG |
| 2 | 1005 | 0.87 | 0.89 | 119 | AGS, MG |
| 3 | 673 | 0.80 | 0.85 | 76 | empty |
| 4 | 603 | 0.79 | 0.85 | 65 | empty |
| 5 | 300 | 0.78 | 0.89 | 50 | empty |
Interfaces
6 interfaces between chains.
- A–B · 7393 Ų buried · 69 hydrogen bonds · protein-protein
- C–D · 7319 Ų buried · 65 hydrogen bonds · protein-protein
- D–F · 600 Ų buried · 5 hydrogen bonds · protein-protein
- B–E · 530 Ų buried · 3 hydrogen bonds · protein-protein
- C–F · 408 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6QUZ · Structure of ATPgS-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 0.73
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 6QUZ · PDBe 6QUZ · UniProt Q9WYC3 · UniProt Q9WYC4
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