Research workbench
Cryo-EM structure of pre-dephosphorylation complex of phosphorylated EIF2ALPHA with trapped holophosphatase (PP1A_D64A/PPP1R15A/G- ACTIN/DNASE I)
Analyse Cryo-EM structure of pre-dephosphorylation complex of phosphorylated EIF2ALPHA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NZM
- Type
- protein
- Length
- 1,157 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Eukaryotic translation initiation factor 2 subunit 1; SERINE/THREONINE-protein…
- EC
- 3.1.3.16, 3.1.21.1
- UniProt
- P05198, P62139, P68135, P00639, O75807
- Ligands
- ATP, NAG, MN
- Pockets
- 13 · best druggability 0.75
Structure
electron microscopy · 5 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Eukaryotic translation initiation factor 2 subunit 1 | protein | 178 | 44% helix, 19% strand | P05198 |
| B | SERINE/THREONINE-protein phosphatase PP1-alpha catalytic subunit (EC 3.1.3.16) | protein | 293 | 34% helix, 17% strand | P62139 |
| A | Actin, alpha skeletal muscle, intermediate form | protein | 370 | 44% helix, 21% strand | P68135 |
| D | Deoxyribonuclease-1 (EC 3.1.21.1) | protein | 257 | 30% helix, 26% strand | P00639 |
| C | Protein phosphatase 1 regulatory subunit 15A, MALTOSE/MALTODEXTRIN-binding periplasmic protein | protein | 59 | 56% helix, 7% strand | O75807 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains D
- MN · Manganese (II) ion · metal · chains E, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 470 | 0.75 | 0.84 | 50 | ATP |
| 2 | 178 | 0.67 | 0.87 | 30 | empty |
| 3 | 252 | 0.67 | 0.84 | 40 | empty |
| 4 | 53 | 0.67 | 0.95 | 16 | empty |
| 5 | 575 | 0.65 | 0.76 | 58 | empty |
Interfaces
8 interfaces between chains.
- B–C · 1224 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 1003 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 951 Ų buried · 7 hydrogen bonds · protein-protein
- E–B · 622 Ų buried · 17 hydrogen bonds · protein-protein
- E–C · 525 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 1 glycan, 1 modified (disulfide, N-glycosylation, phosphorylation).
Compared structures
- 7NZM · Cryo-EM structure of pre-dephosphorylation complex of phosphorylated eIF2alpha with… · the same entry in another collection · chain C against C, TM-score 1.00
- P68135 · AlphaFold monomer V2.0 prediction for actin, alpha skeletal muscle (P68135) · a predicted model of the same protein · chain A against A, TM-score 0.97
- P00639 · AlphaFold monomer V2.0 prediction for deoxyribonuclease-1 (P00639) · a predicted model of the same protein · chain D against A, TM-score 0.97
- P62139 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein phosphatase PP1-alpha… · a predicted model of the same protein · chain B against A, TM-score 0.96
- P05198 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 2 subunit… · a predicted model of the same protein · chain E against A, TM-score 0.91
- O75807 · AlphaFold monomer V2.0 prediction for protein phosphatase 1 regulatory subunit 15A… · a predicted model of the same protein · chain C against A, TM-score 0.59
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 P05198
- Every structure of UniProt P62139
- Every structure of UniProt P68135
- Every structure of UniProt P00639
- Every structure of UniProt O75807
- Elsewhere: RCSB PDB 7NZM · PDBe 7NZM · UniProt P05198 · UniProt P62139 · UniProt P68135 · UniProt P00639 · UniProt O75807
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.