Research workbench
V/A-type ATPASE/SYNTHASE from thermus thermophilus, rotational state 2
Analyse V/A-type ATPASE/SYNTHASE from thermus thermophilus, rotational state 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y5Z
- Type
- protein
- Length
- 5,852 residues
- Chains
- 26
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- V-type ATP synthase alpha chain; V-type ATP synthase beta chain; V-type ATP synthase…
- EC
- 3.6.3.14
- UniProt
- Q56403, Q56404, O87880, P74903, Q5SIT5, P74901, P74902, Q5SIT6, Q5SIT7
- Ligands
- ADP
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 9 distinct chains · 52% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | V-type ATP synthase alpha chain (EC 3.6.3.14) | protein | 577 | 32% helix, 15% strand | Q56403 |
| D, E, F | V-type ATP synthase beta chain | protein | 459 | 28% helix, 12% strand | Q56404 |
| G | V-type ATP synthase subunit D | protein | 210 | 70% helix, 5% strand | O87880 |
| H | V-type ATP synthase subunit F | protein | 100 | 38% helix, 2% strand | P74903 |
| I, K | V-type ATP synthase, subunit (vapc-therm) | protein | 100 | 92% helix, 0% strand | Q5SIT5 |
| J, L | V-type ATP synthase subunit E | protein | 185 | 71% helix, 3% strand | P74901 |
| M | V-type ATP synthase subunit C | protein | 320 | 68% helix, 0% strand | P74902 |
| N | V-type ATP synthase subunit I | protein | 632 | 59% helix, 6% strand | Q5SIT6 |
| O, P, Q, R, S, T, U, V, W, X, Y, Z | V-type ATP synthase, subunit K | protein | 76 | 82% helix, 0% strand | Q5SIT7 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains B, D, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1050 | 0.81 | 0.83 | 179 | empty |
| 2 | 322 | 0.73 | 0.87 | 58 | empty |
| 3 | 1183 | 0.72 | 0.76 | 241 | empty |
| 4 | 999 | 0.71 | 0.76 | 156 | empty |
| 5 | 266 | 0.70 | 0.86 | 54 | empty |
Interfaces
38 interfaces between chains.
- B–D · 544 Ų buried · 10 hydrogen bonds · protein-protein
- O–Z · 498 Ų buried · 0 hydrogen bonds · protein-protein
- C–E · 485 Ų buried · 5 hydrogen bonds · protein-protein
- Y–Z · 475 Ų buried · 0 hydrogen bonds · protein-protein
- T–U · 465 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5Y5Z · V/A-type ATPase/synthase from Thermus thermophilus, rotational state 2 · 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 Q56403
- Every structure of UniProt Q56404
- Every structure of UniProt O87880
- Every structure of UniProt P74903
- Every structure of UniProt Q5SIT5
- Every structure of UniProt P74901
- Every structure of UniProt P74902
- Every structure of UniProt Q5SIT6
- Every structure of UniProt Q5SIT7
- Elsewhere: RCSB PDB 5Y5Z · PDBe 5Y5Z · UniProt Q56403 · UniProt Q56404 · UniProt O87880 · UniProt P74903 · UniProt Q5SIT5 · UniProt P74901 · UniProt P74902 · UniProt Q5SIT6 · UniProt Q5SIT7
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