Research workbench
Cryoem structures of reconstituted V-ATPase, STATE3
Analyse Cryoem structures of reconstituted V-ATPase, STATE3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7FDC
- Type
- protein
- Length
- 8,295 residues
- Chains
- 31
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yeast vacuolar ATPase a subunit; V-type proton ATPase subunit B; V-type proton ATPase…
- EC
- 7.1.2.2
- UniProt
- P16140, P22203, P32610, P39111, P31412, P41807, Q9UI12, P32563, P32366, P23968, P32842, P25515, Q3E7B6, P53262, P0C5R9
- Pockets
- 20 · best druggability 0.90
Structure
electron microscopy · 19 distinct chains · 51% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Yeast vacuolar ATPase a subunit (EC 7.1.2.2) | protein | 594 | 34% helix, 20% strand | — |
| B | V-type proton ATPase subunit B | protein | 468 | 34% helix, 21% strand | P16140 |
| D | V-type proton ATPase subunit B | protein | 470 | 36% helix, 22% strand | P16140 |
| F | V-type proton ATPase subunit B | protein | 471 | 35% helix, 19% strand | P16140 |
| G, I, K | V-type proton ATPase subunit E | protein | 225 | 72% helix, 6% strand | P22203 |
| H, J, L | V-type proton ATPase subunit G | protein | 111 | 82% helix, 0% strand | — |
| M | V-type proton ATPase subunit D | protein | 218 | 72% helix, 9% strand | P32610 |
| N | V-type proton ATPase subunit F | protein | 115 | 34% helix, 16% strand | P39111 |
| O | V-type proton ATPase subunit C | protein | 392 | 40% helix, 7% strand | P31412 |
| P | Fusion of yeast V-type proton ATPase subunit H(NT) and human V-type proton ATPase subunit H(CT) | protein | 452 | 64% helix, 0% strand | P41807, Q9UI12 |
| Q | Yeast vacuolar ATPase a subunit | protein | 747 | 54% helix, 4% strand | P32563 |
| S | V-type proton ATPase subunit D | protein | 344 | 58% helix, 0% strand | P32366 |
| T | V-type proton ATPase subunit C'' | protein | 200 | 74% helix, 0% strand | P23968 |
| U | V-type proton ATPase subunit C' | protein | 157 | 76% helix, 0% strand | P32842 |
| V, W, X, Z, a, c | V-type proton ATPase subunit C | protein | 159 | 77% helix, 0% strand | P25515 |
| Y, b | V-type proton ATPase subunit C | protein | 160 | 75% helix, 0% strand | P25515 |
| d | V-type proton ATPase subunit E | protein | 69 | 49% helix, 0% strand | Q3E7B6 |
| e | V0 assembly protein 1 | protein | 52 | 46% helix, 0% strand | P53262 |
| f | Yeast vacuolar ATPase F subunit | protein | 76 | 50% helix, 0% strand | P0C5R9 |
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 | 941 | 0.90 | 0.92 | 129 | empty |
| 2 | 1162 | 0.90 | 0.91 | 150 | empty |
| 3 | 1090 | 0.90 | 0.91 | 123 | empty |
| 4 | 1033 | 0.89 | 0.90 | 160 | empty |
| 5 | 871 | 0.88 | 0.90 | 118 | empty |
Interfaces
71 interfaces between chains.
- C–D · 2794 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 2759 Ų buried · 37 hydrogen bonds · protein-protein
- K–L · 2585 Ų buried · 19 hydrogen bonds · protein-protein
- I–J · 2498 Ų buried · 16 hydrogen bonds · protein-protein
- B–I · 2227 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 7FDC · CryoEM Structures of Reconstituted V-ATPase, state3 · the same entry in another collection · chain F against F, 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 P16140
- Every structure of UniProt P22203
- Every structure of UniProt P32610
- Every structure of UniProt P39111
- Every structure of UniProt P31412
- Every structure of UniProt P41807
- Every structure of UniProt Q9UI12
- Every structure of UniProt P32563
- Every structure of UniProt P32366
- Every structure of UniProt P23968
- Every structure of UniProt P32842
- Every structure of UniProt P25515
- Every structure of UniProt Q3E7B6
- Every structure of UniProt P53262
- Every structure of UniProt P0C5R9
- Elsewhere: RCSB PDB 7FDC · PDBe 7FDC · UniProt P16140 · UniProt P22203 · UniProt P32610 · UniProt P39111 · UniProt P31412 · UniProt P41807 · UniProt Q9UI12 · UniProt P32563 · UniProt P32366 · UniProt P23968 · UniProt P32842 · UniProt P25515 · UniProt Q3E7B6 · UniProt P53262 · UniProt P0C5R9
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