MolNFT v1 · #135777 · protein
Structure of the open conformation of 4-coumarate-CoA ligase from nicotiana tabacum
5U95 · 4-coumarate--CoA ligase 2: “Structure of the open conformation of 4-coumarate-CoA ligase from nicotiana tabacum”. X-ray diffraction, 1 ligand (CA), 20 pockets (best druggability 0.77). MolNFT v1 #135777 on GenesisL1: 3D structure…
- PDB
- 5U95
- Type
- protein
- Length
- 1,975 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-coumarate--CoA ligase 2
- EC
- 6.2.1.12
- UniProt
- O24146
- Ligands
- CA
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-coumarate--CoA ligase 2 (EC 6.2.1.12) | protein | 424 | 33% helix, 22% strand | O24146 |
| B | 4-coumarate--CoA ligase 2 (EC 6.2.1.12) | protein | 527 | 31% helix, 23% strand | O24146 |
| C | 4-coumarate--CoA ligase 2 (EC 6.2.1.12) | protein | 522 | 31% helix, 22% strand | O24146 |
| D | 4-coumarate--CoA ligase 2 (EC 6.2.1.12) | protein | 502 | 32% helix, 22% strand | O24146 |
Ligands and binding sites
- CA · Calcium ion · metal · 5 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 661 | 0.77 | 0.82 | 58 | CA |
| 2 | 635 | 0.75 | 0.81 | 52 | empty |
| 3 | 818 | 0.73 | 0.78 | 83 | empty |
| 4 | 786 | 0.71 | 0.77 | 59 | empty |
| 5 | 259 | 0.70 | 0.85 | 47 | empty |
Interfaces
4 interfaces between chains.
- A–D · 581 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 538 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 409 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 267 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5U95 · Structure of the open conformation of 4-coumarate-CoA ligase from Nicotiana tabacum · the same entry in another collection · chain D against D, TM-score 1.00
- O24146 · AlphaFold monomer V2.0 prediction for 4-coumarate--CoA ligase 2 (O24146) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O24146
- Elsewhere: RCSB PDB 5U95 · PDBe 5U95 · UniProt O24146
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