Research workbench
The vo region of human V-ATPase in state 1 (focused refinement)
Analyse The vo 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
- 6WLW
- Type
- protein
- Length
- 2,749 residues
- Chains
- 16
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- V-type proton ATPase 21 kda proteolipid subunit; V-type proton ATPase 16 kda proteolipid…
- EC
- 3.1.-.-
- UniProt
- Q99437, P27449, P61421, Q93050, O15342, Q6P5S7, Q15904, O75787
- Ligands
- PTY, WSS, CLR, WJS, PSF, WJP, NAG, MAN, GAL, GLC, NGA, SIA, BGC, BMA
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 8 distinct chains · 59% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 0 | V-type proton ATPase 21 kda proteolipid subunit | protein | 204 | 83% helix, 0% strand | Q99437 |
| 1, 2, 3, 4, 5, 6, 7, 8, 9 | V-type proton ATPase 16 kda proteolipid subunit | protein | 150 | 85% helix, 0% strand | P27449 |
| Q | V-type proton ATPase subunit D 1 | protein | 350 | 50% helix, 1% strand | P61421 |
| R | V-type proton ATPase 116 kda subunit a isoform 1 | protein | 428 | 63% helix, 2% strand | Q93050 |
| S | V-type proton ATPase subunit E 1 | protein | 77 | 70% helix, 4% strand | O15342 |
| T | Ribonuclease kappa (EC 3.1.-.-) | protein | 85 | 71% helix, 0% strand | Q6P5S7 |
| U | V-type proton ATPase subunit S1 | protein | 205 | 14% helix, 43% strand | Q15904 |
| V | Renin receptor | protein | 50 | 54% helix, 0% strand | O75787 |
Ligands and binding sites
- PTY · Phosphatidylethanolamine · ligand · 13 copies · chains 0, 9, Q, U, 2, 3, 5, 6, 7, 8, R, S, 1, 4, V
- WSS · tri(methyl)-[2-[[(2~{R})-2-[(~{Z})-octadec-9-enoyl]oxy-3-[(~{E})-1-oxidanylideneoctadec-9-enoxy]propoxy]-oxidanyl-phosphoryl]oxyethyl]azanium · ligand · 10 copies · chains 0, 5, 6, U, 7, 8, V, 1, 2, 3, 4, R, S, T, 9
- CLR · Cholesterol · ligand · 4 copies · chains 4, 5, V, R, S, 0, U
- WJS · (2~{S})-2-$l^{4}-azanyl-3-[[(2~{R})-3-octadecanoyloxy-2-oxidanyl-propoxy]-oxidanyl-oxidanylidene-$l^{6}-phosphanyl]oxy-propanoic acid · ligand · chains 2, 3, V
- PSF · 1,2-dicaproyl-sn-phosphatidyl-L-serine · ligand · chains 4, R
- WJP · Methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6, 10,14,18-tetraen-1-yl dihydrogen diphosphate · ligand · chains 3, 4, R
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains R, S, T, U, V
- MAN · alpha-D-mannopyranose · sugar · 5 copies · chains R, S, 4
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains R, 3
- GLC · alpha-D-glucopyranose · sugar · 3 copies · chains R
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 2 copies · chains R, 3
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies · chains R, 3
- BGC · beta-D-glucopyranose · sugar · chains R
- BMA · beta-D-mannopyranose · sugar · chains 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 941 | 0.83 | 0.83 | 66 | WSS, PTY, WJS |
| 2 | 1163 | 0.80 | 0.81 | 74 | NAG, WJP |
| 3 | 887 | 0.78 | 0.80 | 68 | empty |
| 4 | 552 | 0.76 | 0.83 | 65 | WSS |
| 5 | 622 | 0.76 | 0.81 | 48 | PSF |
Interfaces
36 interfaces between chains.
- R–S · 2592 Ų buried · 28 hydrogen bonds · protein-protein
- 0–9 · 1823 Ų buried · 2 hydrogen bonds · protein-protein
- 0–1 · 1702 Ų buried · 5 hydrogen bonds · protein-protein
- 3–4 · 1640 Ų buried · 3 hydrogen bonds · protein-protein
- 1–2 · 1627 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 glycan, 1 covalent, 1 disulfide (N-glycosylation, covalent ligand, disulfide, glycosylation).
Compared structures
- 6WLW · The Vo region of human V-ATPase in state 1 (focused refinement) · the same entry in another collection · chain 9 against 9, 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 Q99437
- Every structure of UniProt P27449
- Every structure of UniProt P61421
- Every structure of UniProt Q93050
- Every structure of UniProt O15342
- Every structure of UniProt Q6P5S7
- Every structure of UniProt Q15904
- Every structure of UniProt O75787
- Elsewhere: RCSB PDB 6WLW · PDBe 6WLW · UniProt Q99437 · UniProt P27449 · UniProt P61421 · UniProt Q93050 · UniProt O15342 · UniProt Q6P5S7 · UniProt Q15904 · UniProt O75787
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