Research workbench
Crystal structure of the AMP-pnp-bound mutant A(S23C)3B(N64C)3 complex from enterococcus hirae V-ATPase
Analyse Crystal structure of the AMP-pnp-bound mutant A(S23C)3B(N64C)3 complex from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DQD
- Type
- protein
- Length
- 6,177 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- V-type sodium ATPase catalytic subunit a; V-type sodium ATPase subunit B
- EC
- 7.2.2.1
- UniProt
- Q08636, Q08637
- Ligands
- ANP, MG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 7 distinct chains · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | V-type sodium ATPase catalytic subunit a (EC 7.2.2.1) | protein | 584 | 36% helix, 22% strand | Q08636 |
| B, C, J, K | V-type sodium ATPase catalytic subunit a (EC 7.2.2.1) | protein | 584 | 37% helix, 20% strand | Q08636 |
| D, L | V-type sodium ATPase subunit B | protein | 447 | 35% helix, 20% strand | Q08637 |
| E, M | V-type sodium ATPase subunit B | protein | 453 | 36% helix, 19% strand | Q08637 |
| F | V-type sodium ATPase subunit B | protein | 445 | 36% helix, 19% strand | Q08637 |
| I | V-type sodium ATPase catalytic subunit a (EC 7.2.2.1) | protein | 583 | 36% helix, 22% strand | Q08636 |
| N | V-type sodium ATPase subunit B | protein | 429 | 34% helix, 20% strand | Q08637 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 4 copies · chains B, E, C, F, J, M, K, N
- MG · Magnesium ion · metal · 4 copies · chains B, E, C, J, K
- GOL · Glycerol · additive · chains 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 | 1101 | 0.85 | 0.86 | 112 | empty |
| 2 | 1084 | 0.85 | 0.86 | 134 | empty |
| 3 | 680 | 0.85 | 0.89 | 65 | empty |
| 4 | 504 | 0.84 | 0.91 | 62 | empty |
| 5 | 552 | 0.84 | 0.89 | 78 | empty |
Interfaces
19 interfaces between chains.
- K–N · 2918 Ų buried · 34 hydrogen bonds · protein-protein
- C–F · 2699 Ų buried · 32 hydrogen bonds · protein-protein
- I–L · 2627 Ų buried · 31 hydrogen bonds · protein-protein
- A–D · 2596 Ų buried · 40 hydrogen bonds · protein-protein
- J–M · 2505 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 7DQD · Crystal structure of the AMP-PNP-bound mutant A(S23C)3B(N64C)3 complex from enterococcus… · the same entry in another collection · chain N against N, 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 Q08636
- Every structure of UniProt Q08637
- Elsewhere: RCSB PDB 7DQD · PDBe 7DQD · UniProt Q08636 · UniProt Q08637
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