MolNFT v2 · #117043 · protein
ATP synthase from Paracoccus denitrificans
5DN6: “ATP synthase from Paracoccus denitrificans”. X-ray diffraction at 3.98, 3 ligands (ATP, ADP, MG). MolNFT v2 #117043 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5DN6
- Type
- protein
- Length
- 4,682 residues
- Chains
- 29
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.98
- Source
- Paracoccus denitrificans
- UniProt
- A1B8N8, A1B8P0, A1B8N9, A1B8N7, A1B8P1, A1B618, A1B619, A1B602
- Ligands
- ATP, ADP, MG
Structure
x-ray diffraction · resolution 3.98 · 18 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | — | protein | 20 | — | — |
| 2 | — | protein | 15 | — | — |
| 3 | — | protein | 19 | — | — |
| A | — | protein | 505 | — | A1B8N8 |
| B | — | protein | 496 | — | A1B8N8 |
| C | — | protein | 484 | — | A1B8N8 |
| D | — | protein | 470 | — | A1B8P0 |
| E | — | protein | 466 | — | A1B8P0 |
| F | — | protein | 466 | — | A1B8P0 |
| G | — | protein | 260 | — | A1B8N9 |
| H | — | protein | 110 | — | A1B8N7 |
| I | — | protein | 75 | — | A1B8P1 |
| J, K, L, M, N, O, P, Q, R, S, T, U | — | protein | 74 | — | A1B618 |
| V | — | protein | 78 | — | — |
| W | — | protein | 124 | — | — |
| X | — | protein | 98 | — | A1B619 |
| Y | — | protein | 54 | — | — |
| Z | — | protein | 54 | — | A1B602 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, D, C, F, B
- ADP · Adenosine-5'-diphosphate · ligand · chains B, E
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Compared structures
- 5DN6 · ATP synthase from paracoccus denitrificans · 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 A1B8N8
- Every structure of UniProt A1B8P0
- Every structure of UniProt A1B8N9
- Every structure of UniProt A1B8N7
- Every structure of UniProt A1B8P1
- Every structure of UniProt A1B618
- Every structure of UniProt A1B619
- Every structure of UniProt A1B602
- Elsewhere: RCSB PDB 5DN6 · PDBe 5DN6 · UniProt A1B8N8 · UniProt A1B8P0 · UniProt A1B8N9 · UniProt A1B8N7 · UniProt A1B8P1 · UniProt A1B618 · UniProt A1B619 · UniProt A1B602
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