MolNFT v1 · #143740 · protein
Mosaic model of yeast mitochondrial ATP synthase monomer
6B8H · ATP synthase subunit 9, mitochondrial: “Mosaic model of yeast mitochondrial ATP synthase monomer”. Electron microscopy, 2 ligands (ANP, MG), 20 pockets (best druggability 0.89). MolNFT v1 #143740 on GenesisL1: 3D structure, binding…
- PDB
- 6B8H
- Type
- protein
- Length
- 10,470 residues
- Chains
- 60
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP synthase subunit 9, mitochondrial; ATP synthase protein 8; ATP synthase subunit a…
- EC
- 3.6.3.14
- UniProt
- P61829, P00856, P00854, P05626, P30902, Q06405, P81450, P81451, P07251, P00830, P38077, Q12165, E9P9X4, P09457
- Ligands
- ANP, MG
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 23 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1, 2, 4, 5, 8, 0, L, M, P, Q, T, J | ATP synthase subunit 9, mitochondrial | protein | 75 | 85% helix, 0% strand | P61829 |
| 3, 6, 9, N, R, U | ATP synthase subunit 9, mitochondrial | protein | 74 | 86% helix, 0% strand | P61829 |
| 7, S | ATP synthase subunit 9, mitochondrial | protein | 73 | 95% helix, 0% strand | P61829 |
| A, V | ATP synthase protein 8 | protein | 48 | 81% helix, 0% strand | P00856 |
| a, p | ATP synthase subunit a | protein | 249 | 68% helix, 1% strand | P00854 |
| b, q | ATP synthase subunit 4, mitochondrial | protein | 200 | 83% helix, 0% strand | P05626 |
| d, r | ATP synthase subunit D, mitochondrial | protein | 157 | 46% helix, 1% strand | P30902 |
| e, s | ATP synthase subunit E, mitochondrial | protein | 49 | 94% helix, 0% strand | — |
| f, t | ATP synthase subunit F, mitochondrial | protein | 84 | 57% helix, 0% strand | Q06405 |
| g, u | Aatp synthase subunit G | protein | 106 | 81% helix, 0% strand | — |
| i, w | ATP synthase subunit J, mitochondrial | protein | 59 | 36% helix, 0% strand | P81450 |
| k, x | ATP synthase subunit K, mitochondrial | protein | 24 | 38% helix, 0% strand | P81451 |
| K, n | ATP synthase subunit alpha, mitochondrial | protein | 501 | 40% helix, 22% strand | P07251 |
| B, W | ATP synthase subunit alpha, mitochondrial | protein | 492 | 37% helix, 20% strand | P07251 |
| C, X | ATP synthase subunit alpha, mitochondrial | protein | 500 | 41% helix, 20% strand | P07251 |
| D, Y | ATP synthase subunit beta, mitochondrial (EC 3.6.3.14) | protein | 470 | 38% helix, 21% strand | P00830 |
| E, Z | ATP synthase subunit beta, mitochondrial (EC 3.6.3.14) | protein | 468 | 36% helix, 20% strand | P00830 |
| F, c | ATP synthase subunit beta, mitochondrial (EC 3.6.3.14) | protein | 469 | 37% helix, 20% strand | P00830 |
| G, j | ATP synthase subunit gamma, mitochondrial | protein | 265 | 60% helix, 12% strand | P38077 |
| H, l | ATP synthase subunit delta, mitochondrial | protein | 119 | 24% helix, 27% strand | Q12165 |
| I, m | ATP synthase catalytic sector F1 epsilon subunit | protein | 48 | 17% helix, 15% strand | E9P9X4 |
| O, o | ATP synthase subunit 5, mitochondrial | protein | 161 | 58% helix, 0% strand | P09457 |
| h, v | ATP synthase subunit H | protein | 21 | 90% helix, 0% strand | — |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 10 copies · chains K, D, B, E, C, F, n, Y, W, Z, X, c
- MG · Magnesium ion · metal · 10 copies · chains K, B, C, D, F, n, W, X, Y, c
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 | 1103 | 0.89 | 0.91 | 149 | ANP, MG |
| 2 | 714 | 0.87 | 0.91 | 94 | ANP, MG |
| 3 | 824 | 0.86 | 0.89 | 97 | ANP, MG |
| 4 | 649 | 0.86 | 0.91 | 74 | ANP, MG |
| 5 | 959 | 0.84 | 0.86 | 97 | ANP, MG |
Interfaces
142 interfaces between chains.
- B–F · 2752 Ų buried · 39 hydrogen bonds · protein-protein
- W–c · 2748 Ų buried · 38 hydrogen bonds · protein-protein
- K–D · 2486 Ų buried · 32 hydrogen bonds · protein-protein
- n–Y · 2475 Ų buried · 32 hydrogen bonds · protein-protein
- C–F · 2340 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 6B8H · Mosaic model of yeast mitochondrial ATP synthase monomer · the same entry in another collection · chain 0 against 0, 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 P61829
- Every structure of UniProt P00856
- Every structure of UniProt P00854
- Every structure of UniProt P05626
- Every structure of UniProt P30902
- Every structure of UniProt Q06405
- Every structure of UniProt P81450
- Every structure of UniProt P81451
- Every structure of UniProt P07251
- Every structure of UniProt P00830
- Every structure of UniProt P38077
- Every structure of UniProt Q12165
- Every structure of UniProt E9P9X4
- Every structure of UniProt P09457
- Elsewhere: RCSB PDB 6B8H · PDBe 6B8H · UniProt P61829 · UniProt P00856 · UniProt P00854 · UniProt P05626 · UniProt P30902 · UniProt Q06405 · UniProt P81450 · UniProt P81451 · UniProt P07251 · UniProt P00830 · UniProt P38077 · UniProt Q12165 · UniProt E9P9X4 · UniProt P09457
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