MolNFT v1 · #117111 · protein
Structure of P97 N-D1 wild-type in complex with ADP
5DYI · Transitional endoplasmic reticulum ATPase: “Structure of P97 N-D1 wild-type in complex with ADP”. X-ray diffraction, 1 ligand (ADP), 20 pockets (best druggability 0.82). MolNFT v1 #117111 on GenesisL1: 3D structure, binding sites…
- PDB
- 5DYI
- Type
- protein
- Length
- 5,265 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transitional endoplasmic reticulum ATPase
- EC
- 3.6.4.6
- UniProt
- P55072
- Ligands
- ADP
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 440 | 38% helix, 23% strand | P55072 |
| B, C, E, F, G, L | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 438 | 37% helix, 23% strand | P55072 |
| D, H, I, K | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 439 | 37% helix, 23% strand | P55072 |
| J | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 441 | 36% helix, 23% strand | P55072 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
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 | 1136 | 0.82 | 0.83 | 128 | ADP |
| 2 | 1091 | 0.79 | 0.81 | 90 | ADP |
| 3 | 1058 | 0.79 | 0.81 | 90 | ADP |
| 4 | 1044 | 0.79 | 0.80 | 94 | ADP |
| 5 | 1084 | 0.79 | 0.80 | 95 | ADP |
Interfaces
21 interfaces between chains.
- A–B · 1838 Ų buried · 14 hydrogen bonds · protein-protein
- J–K · 1830 Ų buried · 13 hydrogen bonds · protein-protein
- H–I · 1757 Ų buried · 12 hydrogen bonds · protein-protein
- K–L · 1756 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 1737 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5DYI · Structure of p97 N-D1 wild-type in complex with ADP · the same entry in another collection · chain A against A, 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
- Elsewhere: RCSB PDB 5DYI · PDBe 5DYI · UniProt P55072
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