Research workbench
CHLAMYDOMONAS,SPINACH chimeric rubisco
Analyse CHLAMYDOMONAS,SPINACH chimeric rubisco in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1UZD
- Type
- protein
- Length
- 4,767 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribulose bisphosphate carboxylase large chain; Ribulose bisphosphate carboxylase small…
- EC
- 4.1.1.39
- UniProt
- A0A218N8A3, P00873, Q43832
- Ligands
- CAP, MG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, R | Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 465 | 45% helix, 17% strand | A0A218N8A3 |
| B | Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 467 | 44% helix, 17% strand | A0A218N8A3 |
| C, F, I, J, M, P, T, W | Ribulose bisphosphate carboxylase small chain 1, CHLOROPLASTIC,RIBULOSE bisphosphate carboxylase small chain 2, CHLOROPLASTIC,RIBULOSE bisphosphate carboxylase small chain 1, chloroplastic (EC 4.1.1.39) | protein | 129 | 22% helix, 24% strand | P00873, Q43832 |
| H, K, O | Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 469 | 43% helix, 17% strand | A0A218N8A3 |
| V | Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 466 | 44% helix, 17% strand | A0A218N8A3 |
Ligands and binding sites
- CAP · 2-carboxyarabinitol-1,5-diphosphate · ligand · 8 copies · chains A, B, E, K, H, R, O, V
- MG · Magnesium ion · metal · 8 copies · chains A, B, E, K, H, R, O, V
- EDO · 1,2-ethanediol · additive · 54 copies · chains A, B, C, V, E, K, F, H, R, I, J, M, O, P, T, W
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 | 144 | 0.81 | 0.98 | 44 | MG, CAP |
| 2 | 145 | 0.81 | 0.98 | 46 | CAP, EDO |
| 3 | 143 | 0.80 | 0.97 | 43 | MG, CAP, EDO |
| 4 | 128 | 0.80 | 0.98 | 42 | CAP, EDO |
| 5 | 902 | 0.79 | 0.81 | 77 | empty |
Interfaces
48 interfaces between chains.
- A–B · 4837 Ų buried · 89 hydrogen bonds · protein-protein
- H–R · 4829 Ų buried · 88 hydrogen bonds · protein-protein
- O–V · 4825 Ų buried · 91 hydrogen bonds · protein-protein
- E–K · 4815 Ų buried · 92 hydrogen bonds · protein-protein
- K–P · 1922 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 modified, 4 disulfide (hydroxylation, methylation, carboxylation, disulfide).
Compared structures
- 1UZD · Chlamydomonas,Spinach Chimeric Rubisco · the same entry in another collection · chain W against W, 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 A0A218N8A3
- Every structure of UniProt P00873
- Every structure of UniProt Q43832
- Elsewhere: RCSB PDB 1UZD · PDBe 1UZD · UniProt A0A218N8A3 · UniProt P00873 · UniProt Q43832
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