MolNFT v1 · #114824 · protein
P97 variant 2 in the apo state
5C19 · Transitional endoplasmic reticulum ATPase: “P97 variant 2 in the apo state”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.85). MolNFT v1 #114824 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5C19
- Type
- protein
- Length
- 4,191 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
- SO4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 734 | 37% helix, 16% strand | P55072 |
| B | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 729 | 41% helix, 17% strand | P55072 |
| C | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 729 | 42% helix, 17% strand | P55072 |
| D | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 553 | 41% helix, 10% strand | P55072 |
| E, F | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 723 | 42% helix, 17% strand | P55072 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 12 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 | 870 | 0.85 | 0.87 | 106 | SO4 |
| 2 | 623 | 0.83 | 0.87 | 89 | empty |
| 3 | 799 | 0.82 | 0.85 | 109 | empty |
| 4 | 628 | 0.82 | 0.87 | 82 | empty |
| 5 | 558 | 0.81 | 0.87 | 81 | empty |
Interfaces
10 interfaces between chains.
- A–F · 3909 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 3821 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 3643 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 3638 Ų buried · 29 hydrogen bonds · protein-protein
- E–F · 3463 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 5C19 · p97 variant 2 in the apo state · the same entry in another collection · chain C against C, 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 5C19 · PDBe 5C19 · UniProt P55072
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