Research workbench
Structure of four mutant forms of yeast F1 ATPase: gamma-I270T
Analyse Structure of four mutant forms of yeast F1 ATPase: gamma-I270T in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OE7
- Type
- protein
- Length
- 9,591 residues
- Chains
- 27
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP synthase subunit alpha; ATP synthase subunit beta; ATP synthase subunit gamma; ATP…
- EC
- 3.6.3.14
- UniProt
- P07251, P00830, P38077, Q12165, P21306
- Ligands
- ANP, MG, PO4
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 21 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, L | ATP synthase subunit alpha (EC 3.6.3.14) | protein | 482 | 42% helix, 21% strand | P07251 |
| B | ATP synthase subunit alpha (EC 3.6.3.14) | protein | 483 | 41% helix, 22% strand | P07251 |
| C | ATP synthase subunit alpha (EC 3.6.3.14) | protein | 484 | 41% helix, 21% strand | P07251 |
| D, M, N, V | ATP synthase subunit beta (EC 3.6.3.14) | protein | 470 | 38% helix, 21% strand | P00830 |
| E | ATP synthase subunit beta (EC 3.6.3.14) | protein | 468 | 37% helix, 20% strand | P00830 |
| F, X | ATP synthase subunit beta (EC 3.6.3.14) | protein | 469 | 36% helix, 22% strand | P00830 |
| G | ATP synthase subunit gamma (EC 3.6.3.14) | protein | 265 | 65% helix, 11% strand | P38077 |
| H | ATP synthase subunit delta (EC 3.6.3.14) | protein | 120 | 23% helix, 34% strand | Q12165 |
| I | ATP synthase subunit epsilon (EC 3.6.3.14) | protein | 48 | 31% helix, 17% strand | P21306 |
| J | ATP synthase subunit alpha (EC 3.6.3.14) | protein | 481 | 42% helix, 22% strand | P07251 |
| K | ATP synthase subunit alpha (EC 3.6.3.14) | protein | 486 | 40% helix, 21% strand | P07251 |
| O | ATP synthase subunit beta (EC 3.6.3.14) | protein | 468 | 37% helix, 22% strand | P00830 |
| P | ATP synthase subunit gamma (EC 3.6.3.14) | protein | 244 | 61% helix, 11% strand | P38077 |
| Q | ATP synthase subunit delta (EC 3.6.3.14) | protein | 84 | 19% helix, 7% strand | Q12165 |
| R | ATP synthase subunit epsilon (EC 3.6.3.14) | protein | 31 | 29% helix, 3% strand | P21306 |
| S | ATP synthase subunit alpha (EC 3.6.3.14) | protein | 480 | 41% helix, 22% strand | P07251 |
| T, U | ATP synthase subunit alpha (EC 3.6.3.14) | protein | 481 | 40% helix, 21% strand | P07251 |
| W | ATP synthase subunit beta (EC 3.6.3.14) | protein | 467 | 37% helix, 21% strand | P00830 |
| Y | ATP synthase subunit gamma (EC 3.6.3.14) | protein | 198 | 64% helix, 5% strand | P38077 |
| Z | ATP synthase subunit delta (EC 3.6.3.14) | protein | 15 | 47% helix, 0% strand | Q12165 |
| 1 | ATP synthase subunit epsilon (EC 3.6.3.14) | protein | 25 | 20% helix, 4% strand | P21306 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 15 copies · chains A, D, B, E, C, F, J, M, K, N, L, O, S, V, T, W, U, X
- MG · Magnesium ion · metal · 15 copies · chains A, B, C, D, F, J, K, L, M, O, S, T, U, V, X
- PO4 · Phosphate ion · ion · chains J, N
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 | 808 | 0.88 | 0.91 | 109 | ANP, MG |
| 2 | 822 | 0.87 | 0.90 | 91 | ANP, MG |
| 3 | 798 | 0.86 | 0.89 | 85 | ANP, MG |
| 4 | 816 | 0.86 | 0.89 | 115 | empty |
| 5 | 1181 | 0.85 | 0.86 | 117 | ANP, MG |
Interfaces
52 interfaces between chains.
- L–M · 3015 Ų buried · 39 hydrogen bonds · protein-protein
- K–O · 2542 Ų buried · 35 hydrogen bonds · protein-protein
- T–X · 2503 Ų buried · 35 hydrogen bonds · protein-protein
- U–X · 2473 Ų buried · 32 hydrogen bonds · protein-protein
- U–V · 2469 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 3OE7 · Structure of four mutant forms of yeast f1 ATPase: gamma-I270T · the same entry in another collection · chain K against K, 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 P07251
- Every structure of UniProt P00830
- Every structure of UniProt P38077
- Every structure of UniProt Q12165
- Every structure of UniProt P21306
- Elsewhere: RCSB PDB 3OE7 · PDBe 3OE7 · UniProt P07251 · UniProt P00830 · UniProt P38077 · UniProt Q12165 · UniProt P21306
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