MolNFT v1 · #103739 · protein
Crystal structure of ECGP123 T69V variant at pH 7.5
4PPK · Monomeric azami green: “Crystal structure of ECGP123 T69V variant at pH 7.5”. X-ray diffraction, 1 ligand (CRQ), 11 pockets (best druggability 0.88). MolNFT v1 #103739 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4PPK
- Type
- protein
- Length
- 860 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Monomeric azami green
- Ligands
- CRQ
- Pockets
- 11 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 4% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Monomeric azami green | protein | 216 | 5% helix, 57% strand | — |
| B | Monomeric azami green | protein | 213 | 5% helix, 58% strand | — |
| C | Monomeric azami green | protein | 217 | 3% helix, 57% strand | — |
| D | Monomeric azami green | protein | 214 | 5% helix, 58% strand | — |
Ligands and binding sites
- CRQ · [2-(3-carbamoyl-1-imino-propyl)-4-(4-hydroxy-benzylidene)-5-oxo-4,5-dihydro-imidazol-1-yl]-acetic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1102 | 0.88 | 0.90 | 120 | empty |
| 2 | 77 | 0.74 | 0.98 | 26 | CRQ |
| 3 | 69 | 0.73 | 0.98 | 25 | CRQ |
| 4 | 70 | 0.73 | 0.98 | 25 | CRQ |
| 5 | 68 | 0.73 | 0.98 | 24 | CRQ |
Interfaces
6 interfaces between chains.
- C–D · 1000 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 983 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 886 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 847 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 172 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor (chromophore).
Compared structures
- 4PPK · Crystal structure of eCGP123 T69V variant at pH 7.5 · 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
- Elsewhere: RCSB PDB 4PPK · PDBe 4PPK
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