MolNFT v1 · #70202 · protein
Crystal structure of human GRP78 (70KDA heat shock protein 5 / bip) ATPase domain in complex with ATP
3LDL · 78 kda glucose-regulated protein: “Crystal structure of human GRP78 (70KDA heat shock protein 5 / bip) ATPase domain in complex with ATP”. X-ray diffraction, 2 ligands (ATP, MG), 6 pockets (best druggability 0.80). MolNFT v1 #70202…
- PDB
- 3LDL
- Type
- protein
- Length
- 762 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 78 kda glucose-regulated protein
- UniProt
- P11021
- Ligands
- ATP, MG
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 78 kda glucose-regulated protein | protein | 381 | 39% helix, 28% strand | P11021 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 766 | 0.80 | 0.83 | 74 | ATP, MG |
| 2 | 704 | 0.79 | 0.83 | 68 | ATP |
| 3 | 996 | 0.74 | 0.77 | 78 | empty |
| 4 | 52 | 0.51 | 0.88 | 15 | empty |
| 5 | 97 | 0.43 | 0.79 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 284 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3LDL · Crystal structure of human GRP78 (70kDa heat shock protein 5 / BIP) ATPase domain in… · the same entry in another collection · chain A against A, TM-score 1.00
- P11021 · AlphaFold monomer V2.0 prediction for endoplasmic reticulum chaperone bip (P11021) · a predicted model of the same protein · chain B against A, TM-score 0.88
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 P11021
- Elsewhere: RCSB PDB 3LDL · PDBe 3LDL · UniProt P11021
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