MolNFT v1 · #168619 · protein
Human V-ATPase in state 3 with sidk and ADP
6WM4 · V-type proton ATPase 116 kda subunit a isoform 1: “Human V-ATPase in state 3 with sidk and ADP”. Electron microscopy, 2 ligands (ADP, NAG), 20 pockets (best druggability 0.87). MolNFT v1 #168619 on GenesisL1: 3D structure, binding…
- PDB
- 6WM4
- Type
- protein
- Length
- 9,209 residues
- Chains
- 35
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- V-type proton ATPase 116 kda subunit a isoform 1; V-type proton ATPase subunit C 1…
- EC
- 3.1.-.-, 7.1.2.2
- UniProt
- Q93050, P21283, P36543, O75348, O15342, Q6P5S7, P38606, P21281, A0A4T1L9X6, Q9Y5K8, Q16864, Q15904, O75787, Q99437, P27449, P61421, Q9UI12
- Ligands
- ADP, NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 19 distinct chains · 55% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | V-type proton ATPase 116 kda subunit a isoform 1 | protein | 753 | 57% helix, 5% strand | Q93050 |
| O | V-type proton ATPase subunit C 1 | protein | 375 | 46% helix, 11% strand | P21283 |
| J, I | V-type proton ATPase subunit E 1 | protein | 225 | 71% helix, 8% strand | P36543 |
| M, L, K | V-type proton ATPase subunit G 1 | protein | 114 | 86% helix, 0% strand | O75348 |
| H | V-type proton ATPase subunit E 1 | protein | 224 | 70% helix, 8% strand | P36543 |
| S | V-type proton ATPase subunit E 1 | protein | 77 | 68% helix, 1% strand | O15342 |
| T | Ribonuclease kappa (EC 3.1.-.-) | protein | 85 | 62% helix, 0% strand | Q6P5S7 |
| B, C, A | V-type proton ATPase catalytic subunit a (EC 7.1.2.2) | protein | 600 | 33% helix, 23% strand | P38606 |
| E, F, D | V-type proton ATPase subunit B, brain isoform | protein | 468 | 34% helix, 21% strand | P21281 |
| Y, X | Sidk | protein | 262 | 68% helix, 0% strand | A0A4T1L9X6 |
| Z | Sidk | protein | 267 | 66% helix, 0% strand | A0A4T1L9X6 |
| G | V-type proton ATPase subunit D | protein | 213 | 73% helix, 8% strand | Q9Y5K8 |
| N | V-type proton ATPase subunit F | protein | 110 | 36% helix, 14% strand | Q16864 |
| U | V-type proton ATPase subunit S1 | protein | 204 | 13% helix, 37% strand | Q15904 |
| V | Renin receptor | protein | 49 | 53% helix, 0% strand | O75787 |
| 0 | V-type proton ATPase 21 kda proteolipid subunit | protein | 204 | 75% helix, 0% strand | Q99437 |
| 1, 2, 3, 4, 5, 6, 7, 8, 9 | V-type proton ATPase 16 kda proteolipid subunit | protein | 150 | 81% helix, 0% strand | P27449 |
| Q | V-type proton ATPase subunit D 1 | protein | 351 | 56% helix, 0% strand | P61421 |
| P | V-type proton ATPase subunit H | protein | 427 | 63% helix, 0% strand | Q9UI12 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains R, S, T, U
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 | 495 | 0.87 | 0.94 | 78 | empty |
| 2 | 464 | 0.86 | 0.93 | 81 | empty |
| 3 | 563 | 0.85 | 0.91 | 68 | empty |
| 4 | 380 | 0.85 | 0.94 | 46 | empty |
| 5 | 735 | 0.85 | 0.88 | 74 | empty |
Interfaces
94 interfaces between chains.
- A–D · 3247 Ų buried · 31 hydrogen bonds · protein-protein
- J–M · 3184 Ų buried · 18 hydrogen bonds · protein-protein
- H–K · 3047 Ų buried · 19 hydrogen bonds · protein-protein
- I–L · 2924 Ų buried · 20 hydrogen bonds · protein-protein
- B–E · 2642 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 glycan, 1 disulfide (N-glycosylation, disulfide).
Compared structures
- 6WM4 · Human V-ATPase in state 3 with SidK and ADP · the same entry in another collection · chain T against T, 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 Q93050
- Every structure of UniProt P21283
- Every structure of UniProt P36543
- Every structure of UniProt O75348
- Every structure of UniProt O15342
- Every structure of UniProt Q6P5S7
- 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 Q15904
- Every structure of UniProt O75787
- Every structure of UniProt Q99437
- Every structure of UniProt P27449
- Every structure of UniProt P61421
- Every structure of UniProt Q9UI12
- Elsewhere: RCSB PDB 6WM4 · PDBe 6WM4 · UniProt Q93050 · UniProt P21283 · UniProt P36543 · UniProt O75348 · UniProt O15342 · UniProt Q6P5S7 · UniProt P38606 · UniProt P21281 · UniProt A0A4T1L9X6 · UniProt Q9Y5K8 · UniProt Q16864 · UniProt Q15904 · UniProt O75787 · UniProt Q99437 · UniProt P27449 · UniProt P61421 · UniProt Q9UI12
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