Research workbench
The crystal structure of arabidopsis 7-hydroxymethyl chlorophyll a reductase (hcar)
Analyse The crystal structure of arabidopsis 7-hydroxymethyl chlorophyll a reductase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DQR
- Type
- protein
- Length
- 2,476 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 7-hydroxymethyl chlorophyll a reductase, chloroplastic
- EC
- 1.17.7.2
- UniProt
- Q8GS60
- Ligands
- SF4, FAD
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 6 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 7-hydroxymethyl chlorophyll a reductase, chloroplastic (EC 1.17.7.2) | protein | 414 | 42% helix, 18% strand | Q8GS60 |
| B | 7-hydroxymethyl chlorophyll a reductase, chloroplastic (EC 1.17.7.2) | protein | 411 | 41% helix, 16% strand | Q8GS60 |
| C | 7-hydroxymethyl chlorophyll a reductase, chloroplastic (EC 1.17.7.2) | protein | 421 | 43% helix, 17% strand | Q8GS60 |
| D | 7-hydroxymethyl chlorophyll a reductase, chloroplastic (EC 1.17.7.2) | protein | 411 | 43% helix, 17% strand | Q8GS60 |
| E | 7-hydroxymethyl chlorophyll a reductase, chloroplastic (EC 1.17.7.2) | protein | 406 | 43% helix, 18% strand | Q8GS60 |
| F | 7-hydroxymethyl chlorophyll a reductase, chloroplastic (EC 1.17.7.2) | protein | 413 | 41% helix, 16% strand | Q8GS60 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 12 copies · chains A, B, C, D, E, F
- FAD · Flavin-adenine dinucleotide · ligand · 6 copies · chains A, B, C, D, E, F
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 | 1107 | 0.90 | 0.92 | 124 | SF4, FAD |
| 2 | 1039 | 0.90 | 0.92 | 122 | SF4, FAD |
| 3 | 977 | 0.90 | 0.91 | 110 | SF4, FAD |
| 4 | 1142 | 0.89 | 0.91 | 109 | SF4, FAD |
| 5 | 1133 | 0.87 | 0.88 | 97 | FAD |
Interfaces
12 interfaces between chains.
- D–E · 858 Ų buried · 4 hydrogen bonds · protein-protein
- E–F · 744 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 719 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 718 Ų buried · 1 hydrogen bond · protein-protein
- D–F · 414 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5DQR · The crystal structure of Arabidopsis 7-hydroxymethyl chlorophyll a reductase (HCAR) · the same entry in another collection · chain F against F, TM-score 1.00
- Q8GS60 · AlphaFold monomer V2.0 prediction for 7-hydroxymethyl chlorophyll a reductase… · a predicted model of the same protein · chain F 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 Q8GS60
- Elsewhere: RCSB PDB 5DQR · PDBe 5DQR · UniProt Q8GS60
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