MolNFT v1 · #108269 · protein
Heterocyclase in complex with substrate and cofactor
4V1U · Lynd: “Heterocyclase in complex with substrate and cofactor”. X-ray diffraction, 3 ligands (AMP, CA, ZN), 19 pockets (best druggability 0.84). MolNFT v1 #108269 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4V1U
- Type
- protein
- Length
- 1,513 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lynd; Pate
- UniProt
- A0YXD2
- Ligands
- AMP, CA, ZN
- Pockets
- 19 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lynd | protein | 746 | 37% helix, 19% strand | A0YXD2 |
| B | Lynd | protein | 743 | 38% helix, 17% strand | A0YXD2 |
| C, D | Pate | protein | 12 | 33% helix, 33% strand | — |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1142 | 0.84 | 0.85 | 129 | AMP, CA |
| 2 | 716 | 0.82 | 0.86 | 69 | AMP, CA |
| 3 | 59 | 0.72 | 0.99 | 19 | empty |
| 4 | 73 | 0.72 | 0.97 | 20 | empty |
| 5 | 300 | 0.72 | 0.85 | 43 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3431 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 667 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 666 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 149 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 140 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4V1U · 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 4V1U · PDBe 4V1U · UniProt A0YXD2
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