Research workbench
Human V-ATPase in state 1 with sidk and ADP
Analyse Human V-ATPase in state 1 with sidk and ADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WM2
- Type
- protein
- Length
- 9,171 residues
- Chains
- 35
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- V-type proton ATPase subunit E 1; V-type proton ATPase subunit G 1; V-type proton ATPase…
- EC
- 7.1.2.2, 3.1.-.-
- UniProt
- P36543, O75348, P21283, Q9UI12, Q93050, P38606, P21281, A0A4T1L9X6, Q9Y5K8, Q16864, Q99437, P27449, P61421, O15342, Q6P5S7, Q15904, O75787
- Ligands
- PTY, WSS, CLR, PSF, WJP, ADP, WJS, NAG, MAN, GAL, GLC, NGA, SIA, BGC, BMA
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 18 distinct chains · 54% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, I, J | V-type proton ATPase subunit E 1 | protein | 225 | 68% helix, 9% strand | P36543 |
| K, L, M | V-type proton ATPase subunit G 1 | protein | 114 | 85% helix, 0% strand | O75348 |
| O | V-type proton ATPase subunit C 1 | protein | 359 | 48% helix, 15% strand | P21283 |
| P | V-type proton ATPase subunit H | protein | 427 | 63% helix, 0% strand | Q9UI12 |
| R | V-type proton ATPase 116 kda subunit a isoform 1 | protein | 753 | 58% helix, 7% strand | Q93050 |
| A, B, C | V-type proton ATPase catalytic subunit a (EC 7.1.2.2) | protein | 600 | 31% helix, 24% strand | P38606 |
| D, E, F | V-type proton ATPase subunit B, brain isoform | protein | 460 | 32% helix, 23% strand | P21281 |
| X, Z | Sidk | protein | 262 | 67% helix, 0% strand | A0A4T1L9X6 |
| Y | Sidk | protein | 267 | 65% helix, 0% strand | A0A4T1L9X6 |
| G | V-type proton ATPase subunit D | protein | 213 | 71% helix, 8% strand | Q9Y5K8 |
| N | V-type proton ATPase subunit F | protein | 110 | 33% helix, 19% strand | Q16864 |
| 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 | 83% helix, 0% strand | P27449 |
| Q | V-type proton ATPase subunit D 1 | protein | 350 | 54% helix, 1% strand | P61421 |
| S | V-type proton ATPase subunit E 1 | protein | 77 | 69% helix, 4% strand | O15342 |
| T | Ribonuclease kappa (EC 3.1.-.-) | protein | 85 | 75% helix, 0% strand | Q6P5S7 |
| U | V-type proton ATPase subunit S1 | protein | 205 | 16% helix, 44% strand | Q15904 |
| V | Renin receptor | protein | 50 | 54% helix, 0% strand | O75787 |
Ligands and binding sites
- PTY · Phosphatidylethanolamine · ligand · 13 copies · chains R, S, 0, 9, Q, U, 2, 3, 5, 6, 7, 8, 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 R, S, T, 0, U, V, 5, 6, 1, 2, 3, 4, 8, 9, 7
- CLR · Cholesterol · ligand · 4 copies · chains R, S, 0, U, V, 4, 5
- PSF · 1,2-dicaproyl-sn-phosphatidyl-L-serine · ligand · chains R, 4
- WJP · Methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6, 10,14,18-tetraen-1-yl dihydrogen diphosphate · ligand · chains R, 3, 4
- ADP · Adenosine-5'-diphosphate · ligand · chains C, F
- 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
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains U, V, R, S, T
- 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1026 | 0.89 | 0.90 | 144 | empty |
| 2 | 774 | 0.88 | 0.92 | 111 | empty |
| 3 | 1059 | 0.87 | 0.87 | 109 | ADP |
| 4 | 616 | 0.85 | 0.90 | 56 | empty |
| 5 | 984 | 0.85 | 0.86 | 104 | empty |
Interfaces
89 interfaces between chains.
- C–F · 3281 Ų buried · 30 hydrogen bonds · protein-protein
- I–L · 3212 Ų buried · 20 hydrogen bonds · protein-protein
- J–M · 3109 Ų buried · 15 hydrogen bonds · protein-protein
- H–K · 3073 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 2776 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 glycan, 2 covalent, 1 disulfide (N-glycosylation, covalent ligand, disulfide).
Compared structures
- 6WM2 · Human V-ATPase in state 1 with SidK and ADP · 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 P36543
- Every structure of UniProt O75348
- Every structure of UniProt P21283
- Every structure of UniProt Q9UI12
- Every structure of UniProt Q93050
- Every structure of UniProt P38606
- Every structure of UniProt P21281
- Every structure of UniProt A0A4T1L9X6
- Every structure of UniProt Q9Y5K8
- Every structure of UniProt Q16864
- Every structure of UniProt Q99437
- Every structure of UniProt P27449
- Every structure of UniProt P61421
- Every structure of UniProt O15342
- Every structure of UniProt Q6P5S7
- Every structure of UniProt Q15904
- Every structure of UniProt O75787
- Elsewhere: RCSB PDB 6WM2 · PDBe 6WM2 · UniProt P36543 · UniProt O75348 · UniProt P21283 · UniProt Q9UI12 · UniProt Q93050 · UniProt P38606 · UniProt P21281 · UniProt A0A4T1L9X6 · UniProt Q9Y5K8 · UniProt Q16864 · UniProt Q99437 · UniProt P27449 · UniProt P61421 · UniProt O15342 · UniProt Q6P5S7 · UniProt Q15904 · UniProt O75787
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