Research workbench
Crystal structure of yeast mitochondrial F1-ATPase
Analyse Crystal structure of yeast mitochondrial F1-ATPase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2HLD
- Type
- protein
- Length
- 9,599 residues
- Chains
- 27
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP synthase alpha chain, mitochondrial; ATP synthase beta chain, mitochondrial; ATP…
- EC
- 3.6.3.14
- UniProt
- P07251, P00830, P38077, Q12165, P21306
- Ligands
- ANP, MG, PO4
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 21 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, L | ATP synthase alpha chain, mitochondrial (EC 3.6.3.14) | protein | 482 | 43% helix, 21% strand | P07251 |
| B | ATP synthase alpha chain, mitochondrial (EC 3.6.3.14) | protein | 483 | 41% helix, 21% strand | P07251 |
| C | ATP synthase alpha chain, mitochondrial (EC 3.6.3.14) | protein | 484 | 42% helix, 21% strand | P07251 |
| D, M, N, V | ATP synthase beta chain, mitochondrial (EC 3.6.3.14) | protein | 470 | 40% helix, 22% strand | P00830 |
| E | ATP synthase beta chain, mitochondrial (EC 3.6.3.14) | protein | 468 | 39% helix, 20% strand | P00830 |
| F, X | ATP synthase beta chain, mitochondrial (EC 3.6.3.14) | protein | 469 | 37% helix, 22% strand | P00830 |
| G | ATP synthase gamma chain, mitochondrial (EC 3.6.3.14) | protein | 265 | 64% helix, 12% strand | P38077 |
| H | ATP synthase delta chain, mitochondrial (EC 3.6.3.14) | protein | 120 | 24% helix, 33% strand | Q12165 |
| I | ATP synthase epsilon chain, mitochondrial (EC 3.6.3.14) | protein | 48 | 35% helix, 17% strand | P21306 |
| J | ATP synthase alpha chain, mitochondrial (EC 3.6.3.14) | protein | 481 | 42% helix, 21% strand | P07251 |
| K | ATP synthase alpha chain, mitochondrial (EC 3.6.3.14) | protein | 486 | 40% helix, 21% strand | P07251 |
| O | ATP synthase beta chain, mitochondrial (EC 3.6.3.14) | protein | 468 | 37% helix, 22% strand | P00830 |
| P | ATP synthase gamma chain, mitochondrial (EC 3.6.3.14) | protein | 243 | 57% helix, 11% strand | P38077 |
| Q | ATP synthase delta chain, mitochondrial (EC 3.6.3.14) | protein | 84 | 21% helix, 12% strand | Q12165 |
| R | ATP synthase epsilon chain, mitochondrial (EC 3.6.3.14) | protein | 34 | 41% helix, 3% strand | P21306 |
| S | ATP synthase alpha chain, mitochondrial (EC 3.6.3.14) | protein | 480 | 42% helix, 22% strand | P07251 |
| T, U | ATP synthase alpha chain, mitochondrial (EC 3.6.3.14) | protein | 481 | 41% helix, 21% strand | P07251 |
| W | ATP synthase beta chain, mitochondrial (EC 3.6.3.14) | protein | 467 | 39% helix, 22% strand | P00830 |
| Y | ATP synthase gamma chain, mitochondrial (EC 3.6.3.14) | protein | 200 | 66% helix, 3% strand | P38077 |
| Z | ATP synthase delta chain, mitochondrial (EC 3.6.3.14) | protein | 17 | 82% helix, 0% strand | Q12165 |
| 1 | ATP synthase epsilon chain, mitochondrial (EC 3.6.3.14) | protein | 27 | 48% 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, 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 | 699 | 0.87 | 0.91 | 79 | MG, ANP |
| 2 | 752 | 0.87 | 0.90 | 89 | MG, ANP |
| 3 | 656 | 0.87 | 0.91 | 79 | MG, ANP |
| 4 | 741 | 0.86 | 0.89 | 81 | MG, ANP |
| 5 | 626 | 0.86 | 0.90 | 85 | MG, ANP |
Interfaces
52 interfaces between chains.
- L–M · 2935 Ų buried · 43 hydrogen bonds · protein-protein
- T–X · 2516 Ų buried · 32 hydrogen bonds · protein-protein
- K–O · 2489 Ų buried · 35 hydrogen bonds · protein-protein
- B–F · 2417 Ų buried · 36 hydrogen bonds · protein-protein
- S–V · 2410 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 2HLD · Crystal structure of yeast mitochondrial F1-ATPase · the same entry in another collection · chain G against G, 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 2HLD · PDBe 2HLD · UniProt P07251 · UniProt P00830 · UniProt P38077 · UniProt Q12165 · UniProt P21306
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