MolNFT v1 · #114823 · protein
P97-DELTA709-728 in complex with ATP-gamma-S
5C18 · Transitional endoplasmic reticulum ATPase: “P97-DELTA709-728 in complex with ATP-gamma-S”. X-ray diffraction, 3 ligands (AGS, MG, CL), 20 pockets (best druggability 0.86). MolNFT v1 #114823 on GenesisL1: 3D structure, binding sites…
- PDB
- 5C18
- Type
- protein
- Length
- 4,338 residues
- Chains
- 6
- 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
- AGS, MG, CL
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 5 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 722 | 45% helix, 18% strand | P55072 |
| B | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 723 | 44% helix, 17% strand | P55072 |
| C | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 724 | 42% helix, 17% strand | P55072 |
| E | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 723 | 44% helix, 17% strand | P55072 |
| F | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 724 | 43% helix, 17% strand | P55072 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 12 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 12 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D, E, F
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 | 964 | 0.86 | 0.87 | 124 | AGS, MG |
| 2 | 565 | 0.81 | 0.87 | 79 | empty |
| 3 | 508 | 0.80 | 0.87 | 71 | AGS, MG |
| 4 | 396 | 0.79 | 0.88 | 53 | empty |
| 5 | 342 | 0.79 | 0.89 | 53 | empty |
Interfaces
6 interfaces between chains.
- C–D · 3691 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 3678 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 3659 Ų buried · 35 hydrogen bonds · protein-protein
- E–F · 3656 Ų buried · 28 hydrogen bonds · protein-protein
- A–F · 3625 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 5C18 · p97-delta709-728 in complex with ATP-gamma-S · 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 5C18 · PDBe 5C18 · UniProt P55072
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