MolNFT v1 · #127277 · protein
Structure of the kdpfabc complex
5MRW · Potassium-transporting ATPase potassium-binding subunit: “Structure of the kdpfabc complex”. X-ray diffraction, 2 ligands (PX4, K), 20 pockets (best druggability 0.79). MolNFT v1 #127277 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5MRW
- Type
- protein
- Length
- 4,335 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Potassium-transporting ATPase potassium-binding subunit; Potassium-transporting ATPase…
- EC
- 3.6.3.12
- UniProt
- P03959, P03960, A0A085P4P2, P36937
- Ligands
- PX4, K
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 57% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, I | Potassium-transporting ATPase potassium-binding subunit | protein | 557 | 64% helix, 2% strand | P03959 |
| B, F, J | Potassium-transporting ATPase ATP-binding subunit (EC 3.6.3.12) | protein | 674 | 53% helix, 15% strand | P03960 |
| C, G, K | Potassium-transporting ATPase kdpc subunit | protein | 187 | 48% helix, 9% strand | A0A085P4P2 |
| D, H, L | Potassium-transporting ATPase kdpf subunit | protein | 27 | 81% helix, 0% strand | P36937 |
Ligands and binding sites
- PX4 · 1,2-dimyristoyl-sn-glycero-3-phosphocholine · ligand · 6 copies · chains A, B, E, F, H, I, J
- K · Potassium ion · metal · 3 copies · chains A, E, I
- BOG · octyl beta-D-glucopyranoside · additive · 4 copies · chains A, B, E, I
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 | 112 | 0.79 | 0.98 | 31 | empty |
| 2 | 106 | 0.79 | 0.98 | 28 | empty |
| 3 | 414 | 0.77 | 0.86 | 43 | empty |
| 4 | 99 | 0.77 | 0.97 | 29 | empty |
| 5 | 682 | 0.76 | 0.81 | 67 | PX4 |
Interfaces
20 interfaces between chains.
- E–G · 4020 Ų buried · 53 hydrogen bonds · protein-protein
- A–C · 4009 Ų buried · 58 hydrogen bonds · protein-protein
- I–K · 3976 Ų buried · 54 hydrogen bonds · protein-protein
- A–B · 2274 Ų buried · 9 hydrogen bonds · protein-protein
- I–J · 2242 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (phosphorylation).
Compared structures
- 5MRW · Structure of the KdpFABC complex · the same entry in another collection · chain L against L, 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 P03959
- Every structure of UniProt P03960
- Every structure of UniProt A0A085P4P2
- Every structure of UniProt P36937
- Elsewhere: RCSB PDB 5MRW · PDBe 5MRW · UniProt P03959 · UniProt P03960 · UniProt A0A085P4P2 · UniProt P36937
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