Research workbench
Structure of P97 N-D1 R155H mutant in complex with ADP
Analyse Structure of P97 N-D1 R155H mutant in complex with ADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KOD
- Type
- protein
- Length
- 5,271 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 0.87
Structure
x-ray diffraction · 9 distinct chains · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 438 | 36% helix, 23% strand | P55072 |
| B | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 439 | 36% helix, 23% strand | P55072 |
| C, F, K | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 438 | 36% helix, 23% strand | P55072 |
| D | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 439 | 36% helix, 23% strand | P55072 |
| E | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 439 | 36% helix, 23% strand | P55072 |
| G | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 437 | 36% helix, 23% strand | P55072 |
| I | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 440 | 35% helix, 23% strand | P55072 |
| J | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 445 | 35% helix, 22% strand | P55072 |
| L | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 442 | 35% helix, 22% strand | P55072 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 12 copies · chains A, E, B, F, C, D, G, K, H, L, I, J
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 | 642 | 0.87 | 0.91 | 76 | empty |
| 2 | 1177 | 0.83 | 0.84 | 143 | ADP |
| 3 | 965 | 0.82 | 0.84 | 115 | ADP |
| 4 | 1020 | 0.82 | 0.83 | 128 | ADP |
| 5 | 860 | 0.81 | 0.83 | 92 | ADP |
Interfaces
23 interfaces between chains.
- H–L · 1666 Ų buried · 13 hydrogen bonds · protein-protein
- H–J · 1660 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 1650 Ų buried · 16 hydrogen bonds · protein-protein
- I–J · 1603 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1603 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 4KOD · Structure of p97 N-D1 R155H mutant 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 4KOD · PDBe 4KOD · UniProt P55072
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