MolNFT v1 · #151081 · protein
Common mode of remodeling aaa atpases P97/CDC48 by their disassembly cofactors ASPL/PUX1
6HD0 · Transitional endoplasmic reticulum ATPase: “Common mode of remodeling aaa atpases P97/CDC48 by their disassembly cofactors ASPL/PUX1”. X-ray diffraction, 1 ligand (ADP), 20 pockets (best druggability 0.84). MolNFT v1 #151081 on…
- PDB
- 6HD0
- Type
- protein
- Length
- 3,086 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transitional endoplasmic reticulum ATPase; Plant ubx domain-containing protein 1
- EC
- 3.6.4.6
- UniProt
- P55072, Q9LK22
- Ligands
- ADP
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 439 | 36% helix, 20% strand | P55072 |
| G, D, E, F, K, I | Plant ubx domain-containing protein 1 | protein | 75 | 19% helix, 35% strand | Q9LK22 |
| T, U, V, A | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 440 | 35% helix, 22% strand | P55072 |
| C | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 437 | 35% helix, 21% strand | P55072 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 6 copies · chains B, C, T, U, V, A
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 | 770 | 0.84 | 0.88 | 118 | ADP |
| 2 | 909 | 0.83 | 0.85 | 120 | ADP |
| 3 | 744 | 0.82 | 0.86 | 110 | ADP |
| 4 | 1155 | 0.82 | 0.83 | 119 | ADP |
| 5 | 499 | 0.79 | 0.86 | 76 | empty |
Interfaces
12 interfaces between chains.
- V–A · 1760 Ų buried · 20 hydrogen bonds · protein-protein
- B–A · 1715 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1686 Ų buried · 16 hydrogen bonds · protein-protein
- U–V · 1678 Ų buried · 20 hydrogen bonds · protein-protein
- T–U · 1649 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6HD0 · Common mode of remodeling AAA ATPases p97/CDC48 by their disassembly cofactors ASPL/PUX1 · the same entry in another collection · chain I against I, 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 P55072
- Every structure of UniProt Q9LK22
- Elsewhere: RCSB PDB 6HD0 · PDBe 6HD0 · UniProt P55072 · UniProt Q9LK22
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