MolNFT v1 · #171774 · protein
Copii on membranes, inner coat
6ZGA · Protein transport protein SEC23: “Copii on membranes, inner coat”. Electron microscopy, 3 ligands (GNP, ZN, MG), 20 pockets (best druggability 0.83). MolNFT v1 #171774 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6ZGA
- Type
- protein
- Length
- 3,413 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein transport protein SEC23; Protein transport protein SEC24; Small copii coat GTPase…
- EC
- 3.6.5.-
- UniProt
- P15303, P40482, P20606
- Ligands
- GNP, ZN, MG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 7 distinct chains · 30% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein transport protein SEC23 | protein | 751 | 31% helix, 20% strand | P15303 |
| B | Protein transport protein SEC24 | protein | 786 | 29% helix, 17% strand | P40482 |
| C | Small copii coat GTPase SAR1 (EC 3.6.5.-) | protein | 168 | 30% helix, 21% strand | P20606 |
| D, H | Pro-pro-pro | protein | 3 | 0% helix, 0% strand | — |
| E | Protein transport protein SEC23 | protein | 750 | 31% helix, 20% strand | P15303 |
| F | Protein transport protein SEC24 | protein | 785 | 31% helix, 17% strand | P40482 |
| G | Small copii coat GTPase SAR1 (EC 3.6.5.-) | protein | 167 | 29% helix, 24% strand | P20606 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains A, C, E, G
- ZN · Zinc ion · metal · 4 copies · chains A, B, E, F
- MG · Magnesium ion · metal · 2 copies · chains C, G
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 | 1024 | 0.83 | 0.84 | 111 | empty |
| 2 | 673 | 0.82 | 0.86 | 77 | empty |
| 3 | 630 | 0.81 | 0.86 | 90 | empty |
| 4 | 418 | 0.80 | 0.88 | 68 | GNP, MG |
| 5 | 135 | 0.77 | 0.94 | 28 | empty |
Interfaces
10 interfaces between chains.
- A–C · 1703 Ų buried · 20 hydrogen bonds · protein-protein
- E–G · 1590 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 1014 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1012 Ų buried · 13 hydrogen bonds · protein-protein
- C–E · 684 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 6ZGA · COPII on membranes, inner coat · the same entry in another collection · chain H against H, TM-score 1.00
- P40482 · AlphaFold monomer V2.0 prediction for protein transport protein SEC24 (P40482) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P15303 · AlphaFold monomer V2.0 prediction for protein transport protein SEC23 (P15303) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P15303
- Every structure of UniProt P40482
- Every structure of UniProt P20606
- Elsewhere: RCSB PDB 6ZGA · PDBe 6ZGA · UniProt P15303 · UniProt P40482 · UniProt P20606
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