MolNFT v1 · #108268 · protein
Heterocyclase in complex with substrate and cofactor
4V1T · Lynd: “Heterocyclase in complex with substrate and cofactor”. X-ray diffraction, 4 ligands (ADP, MG, ZN), 20 pockets (best druggability 0.85). MolNFT v1 #108268 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4V1T
- Type
- protein
- Length
- 1,530 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lynd; Pate
- UniProt
- A0YXD2
- Ligands
- ADP, MG, ZN, PO4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lynd | protein | 748 | 37% helix, 18% strand | A0YXD2 |
| B | Lynd | protein | 753 | 38% helix, 18% strand | A0YXD2 |
| C | Pate | protein | 15 | 27% helix, 27% strand | — |
| D | Pate | protein | 14 | 29% helix, 29% strand | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 6 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1003 | 0.85 | 0.86 | 92 | ADP, MG, PO4 |
| 2 | 1057 | 0.85 | 0.85 | 102 | ADP, MG, PO4 |
| 3 | 77 | 0.75 | 0.98 | 20 | empty |
| 4 | 73 | 0.74 | 0.98 | 18 | empty |
| 5 | 506 | 0.72 | 0.81 | 42 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3424 Ų buried · 53 hydrogen bonds · protein-protein
- A–C · 724 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 711 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 157 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 149 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4V1T · Heterocyclase in complex with substrate and Cofactor · 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
- Every structure of UniProt A0YXD2
- Elsewhere: RCSB PDB 4V1T · PDBe 4V1T · UniProt A0YXD2
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