Research workbench
The V1 region of human V-ATPase in state 1 (focused refinement)
Analyse The V1 region of human V-ATPase in state 1 (focused refinement) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WLZ
- Type
- protein
- Length
- 5,140 residues
- Chains
- 17
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- V-type proton ATPase catalytic subunit a; V-type proton ATPase subunit B, brain isoform…
- EC
- 7.1.2.2
- UniProt
- P38606, P21281, Q5ZWW6, P36543, O75348, Q9Y5K8, Q16864
- Ligands
- ADP
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 8 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | V-type proton ATPase catalytic subunit a (EC 7.1.2.2) | protein | 600 | 32% helix, 24% strand | P38606 |
| D, E, F | V-type proton ATPase subunit B, brain isoform | protein | 460 | 32% helix, 24% strand | P21281 |
| X, Z | Sidk | protein | 262 | 65% helix, 0% strand | Q5ZWW6 |
| Y | Sidk | protein | 267 | 66% helix, 0% strand | Q5ZWW6 |
| J, I, H | V-type proton ATPase subunit E 1 | protein | 193 | 69% helix, 10% strand | P36543 |
| M, L, K | V-type proton ATPase subunit G 1 | protein | 89 | 82% helix, 0% strand | O75348 |
| G | V-type proton ATPase subunit D | protein | 213 | 71% helix, 8% strand | Q9Y5K8 |
| N | V-type proton ATPase subunit F | protein | 110 | 29% helix, 18% strand | Q16864 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains C, F
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 | 816 | 0.89 | 0.92 | 123 | empty |
| 2 | 971 | 0.88 | 0.89 | 97 | empty |
| 3 | 555 | 0.87 | 0.93 | 92 | empty |
| 4 | 1074 | 0.87 | 0.88 | 104 | ADP |
| 5 | 999 | 0.85 | 0.86 | 101 | empty |
Interfaces
41 interfaces between chains.
- C–F · 3259 Ų buried · 32 hydrogen bonds · protein-protein
- A–D · 2768 Ų buried · 24 hydrogen bonds · protein-protein
- J–M · 2553 Ų buried · 14 hydrogen bonds · protein-protein
- H–K · 2549 Ų buried · 8 hydrogen bonds · protein-protein
- I–L · 2320 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6WLZ · The V1 region of human V-ATPase in state 1 (focused refinement) · 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 P38606
- Every structure of UniProt P21281
- Every structure of UniProt Q5ZWW6
- Every structure of UniProt P36543
- Every structure of UniProt O75348
- Every structure of UniProt Q9Y5K8
- Every structure of UniProt Q16864
- Elsewhere: RCSB PDB 6WLZ · PDBe 6WLZ · UniProt P38606 · UniProt P21281 · UniProt Q5ZWW6 · UniProt P36543 · UniProt O75348 · UniProt Q9Y5K8 · UniProt Q16864
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