MolNFT v1 · #164924 · protein
Cryo-EM structure of euglena gracilis mitochondrial ATP synthase, membrane region
6TDV · ATPTB1: “Cryo-EM structure of euglena gracilis mitochondrial ATP synthase, membrane region”. Electron microscopy, 3 ligands (CDL, TRT, LPP), 20 pockets (best druggability 0.86). MolNFT v1 #164924 on GenesisL1: 3D structure, binding…
- PDB
- 6TDV
- Type
- protein
- Length
- 5,464 residues
- Chains
- 38
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATPTB1; ATPTB3; ATPTB6; ATPTB12; Subunit a; Subunit B; Subunit D; Subunit F; Subunit I/J…
- Ligands
- CDL, TRT, LPP
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 19 distinct chains · 59% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, a | ATPTB1 | protein | 486 | 56% helix, 7% strand | — |
| B, b | ATPTB3 | protein | 31 | 87% helix, 0% strand | — |
| D, d | ATPTB6 | protein | 186 | 73% helix, 1% strand | — |
| E, e | ATPTB12 | protein | 96 | 68% helix, 5% strand | — |
| F, f | Subunit a | protein | 274 | 68% helix, 2% strand | — |
| G, g | Subunit B | protein | 111 | 49% helix, 14% strand | — |
| H, h | Subunit D | protein | 388 | 51% helix, 11% strand | — |
| I, i | Subunit F | protein | 97 | 68% helix, 1% strand | — |
| J, j | Subunit I/J | protein | 103 | 64% helix, 1% strand | — |
| K, k | Subunit K | protein | 103 | 65% helix, 1% strand | — |
| L, l | Subunit 8 | protein | 57 | 51% helix, 0% strand | — |
| M, m | ATPEG1 | protein | 166 | 85% helix, 0% strand | — |
| N, n | ATPEG2 | protein | 131 | 40% helix, 1% strand | — |
| O, o | ATPEG3 | protein | 100 | 58% helix, 11% strand | — |
| P, p | ATPEG4 | protein | 114 | 44% helix, 1% strand | — |
| Q, q | ATPEG5 | protein | 89 | 70% helix, 0% strand | — |
| R, r | ATPEG6 | protein | 69 | 38% helix, 6% strand | — |
| S, s | ATPEG7 | protein | 65 | 46% helix, 8% strand | — |
| T, t | ATPEG8 | protein | 66 | 29% helix, 8% strand | — |
Ligands and binding sites
- CDL · Cardiolipin · ligand · 25 copies · chains A, D, O, F, K, J, E, Q, M, f, m, n, p, N, P, R, a, d, o, k, j, e, q, G, I, g, i, r
- TRT · Fragment of triton X-100 · ligand · 16 copies · chains F, G, I, P, n, M, N, g, i, K, R, f, p, m, k, r
- LPP · 2-(hexadecanoyloxy)-1-[(phosphonooxy)methyl]ethyl hexadecanoate · ligand · 12 copies · chains F, K, Q, G, I, P, S, N, i, p, L, O, J, n, R, f, k, q, g, s, l, o, j, r
- LMT · Dodecyl-beta-D-maltoside · additive · 8 copies · chains D, F, J, L, O, G, I, N, f, Q, R, d, j, l, o, g, i, n, q, r
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 | 742 | 0.86 | 0.89 | 87 | LMT |
| 2 | 823 | 0.85 | 0.88 | 104 | LMT |
| 3 | 599 | 0.84 | 0.89 | 76 | empty |
| 4 | 865 | 0.83 | 0.85 | 93 | empty |
| 5 | 735 | 0.82 | 0.85 | 71 | empty |
Interfaces
202 interfaces between chains.
- G–H · 3832 Ų buried · 37 hydrogen bonds · protein-protein
- g–h · 3821 Ų buried · 37 hydrogen bonds · protein-protein
- A–H · 3231 Ų buried · 30 hydrogen bonds · protein-protein
- a–h · 3230 Ų buried · 30 hydrogen bonds · protein-protein
- a–f · 2239 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6TDV · Cryo-EM structure of Euglena gracilis mitochondrial ATP synthase, membrane region · the same entry in another collection · chain B against B, 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
- Elsewhere: RCSB PDB 6TDV · PDBe 6TDV
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