Research workbench
Ovine ATP synthase 1A state
Analyse Ovine ATP synthase 1A state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TT7
- Type
- protein
- Length
- 5,173 residues
- Chains
- 28
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP synthase subunit alpha; ATP synthase subunit beta; ATP synthase subunit gamma; ATP…
- EC
- 7.1.2.2
- UniProt
- W5NY50, W5PEP7, W5PP03, W5Q3H8, W5PTA0, W5QEA9, W5Q0Q5, W5PP37, P17605, O78752, W5P5H1, W5P913, O78751, W5QB48, W5Q5U7, W5PF18
- Ligands
- LHG, ADP, CDL, P5S, S12, MG
- Pockets
- 20 · best druggability 0.90
Structure
electron microscopy · 21 distinct chains · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | ATP synthase subunit alpha | protein | 488 | 38% helix, 21% strand | W5NY50 |
| C | ATP synthase subunit alpha | protein | 503 | 40% helix, 18% strand | W5NY50 |
| A | ATP synthase subunit alpha | protein | 507 | 37% helix, 20% strand | W5NY50 |
| E | ATP synthase subunit beta (EC 7.1.2.2) | protein | 467 | 36% helix, 19% strand | W5PEP7 |
| D | ATP synthase subunit beta (EC 7.1.2.2) | protein | 469 | 34% helix, 21% strand | W5PEP7 |
| F | ATP synthase subunit beta (EC 7.1.2.2) | protein | 472 | 36% helix, 21% strand | W5PEP7 |
| G | ATP synthase subunit gamma | protein | 272 | 61% helix, 11% strand | — |
| H | ATP synthase F1 subunit delta | protein | 132 | 28% helix, 36% strand | W5PP03 |
| I | ATP synthase F1 subunit epsilon | protein | 47 | 60% helix, 9% strand | W5Q3H8 |
| J | ATP synthase peripheral stalk subunit oscp | protein | 188 | 57% helix, 12% strand | W5PTA0 |
| K | ATP synthase subunit B | protein | 208 | 79% helix, 1% strand | W5QEA9 |
| L | ATP synthase-coupling factor 6, mitochondrial | protein | 69 | 45% helix, 0% strand | W5Q0Q5 |
| M | ATP synthase subunit D, mitochondrial | protein | 156 | 54% helix, 1% strand | W5PP37 |
| 1, 2, 3, 4, 5, 6, 7, 8 | ATP synthase F(0) complex subunit C1, mitochondrial | protein | 74 | 86% helix, 0% strand | P17605 |
| N | ATP synthase subunit a | protein | 225 | 73% helix, 0% strand | O78752 |
| O | Subunit dapit | protein | 40 | 60% helix, 0% strand | W5P5H1 |
| P | ATP synthase membrane subunit 6.8PL | protein | 52 | 85% helix, 0% strand | W5P913 |
| Q | ATP synthase protein 8 | protein | 47 | 51% helix, 0% strand | O78751 |
| R | ATP synthase membrane subunit F | protein | 84 | 55% helix, 1% strand | W5QB48 |
| S | ATP synthase subunit | protein | 85 | 72% helix, 1% strand | W5Q5U7 |
| T | Subunit E | protein | 70 | 87% helix, 0% strand | W5PF18 |
Ligands and binding sites
- LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 6 copies · chains K, S, T, R, 2, N, P, Q
- ADP · Adenosine-5'-diphosphate · ligand · 5 copies · chains B, E, C, F, A, D
- CDL · Cardiolipin · ligand · 3 copies · chains K, N, R, P, Q, S
- P5S · O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy) propyl]oxy}(hydroxy)phosphoryl]-L-serine · ligand · chains 1, 2, 3, 4, 5, 6, 7, 8
- S12 · O-[(S)-hydroxy{[(2S)-2-hydroxy-3-(octadec-9-enoyloxy)propyl]oxy}phosphoryl]-L-serine · ligand · chains 1, 2, 3, 4, 6, 7, 8, T
- MG · Magnesium ion · metal · 3 copies · chains B, C, A
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 | 1076 | 0.90 | 0.92 | 113 | P5S, S12 |
| 2 | 670 | 0.86 | 0.90 | 90 | empty |
| 3 | 568 | 0.85 | 0.90 | 94 | empty |
| 4 | 749 | 0.84 | 0.87 | 91 | ADP |
| 5 | 703 | 0.83 | 0.87 | 72 | MG, ADP |
Interfaces
85 interfaces between chains.
- K–M · 3107 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 2877 Ų buried · 34 hydrogen bonds · protein-protein
- A–D · 2673 Ų buried · 22 hydrogen bonds · protein-protein
- C–F · 2560 Ų buried · 22 hydrogen bonds · protein-protein
- B–F · 2490 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 6TT7 · Ovine ATP synthase 1a state · the same entry in another collection · chain M against M, 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 W5NY50
- Every structure of UniProt W5PEP7
- Every structure of UniProt W5PP03
- Every structure of UniProt W5Q3H8
- Every structure of UniProt W5PTA0
- Every structure of UniProt W5QEA9
- Every structure of UniProt W5Q0Q5
- Every structure of UniProt W5PP37
- Every structure of UniProt P17605
- Every structure of UniProt O78752
- Every structure of UniProt W5P5H1
- Every structure of UniProt W5P913
- Every structure of UniProt O78751
- Every structure of UniProt W5QB48
- Every structure of UniProt W5Q5U7
- Every structure of UniProt W5PF18
- Elsewhere: RCSB PDB 6TT7 · PDBe 6TT7 · UniProt W5NY50 · UniProt W5PEP7 · UniProt W5PP03 · UniProt W5Q3H8 · UniProt W5PTA0 · UniProt W5QEA9 · UniProt W5Q0Q5 · UniProt W5PP37 · UniProt P17605 · UniProt O78752 · UniProt W5P5H1 · UniProt W5P913 · UniProt O78751 · UniProt W5QB48 · UniProt W5Q5U7 · UniProt W5PF18
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