Research workbench
L290F mutant rubisco from chlamydomonas
Analyse L290F mutant rubisco from chlamydomonas in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1UWA
- Type
- protein
- Length
- 4,856 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
- P00877, P00873
- Ligands
- CAP, MG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, R, V | Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 465 | 44% helix, 17% strand | P00877 |
| C, F, I, J, M, P, T, W | Ribulose bisphosphate carboxylase small chain 1 (EC 4.1.1.39) | protein | 140 | 27% helix, 22% strand | P00873 |
| E, H, K, O | Ribulose bisphosphate carboxylase large chain (EC 4.1.1.39) | protein | 469 | 44% helix, 17% strand | P00877 |
Ligands and binding sites
- CAP · 2-carboxyarabinitol-1,5-diphosphate · ligand · 8 copies · chains A, O, B, E, H, V, K, R
- MG · Magnesium ion · metal · 8 copies · chains A, O, B, E, H, V, K, R
- EDO · 1,2-ethanediol · additive · 59 copies · chains A, O, M, B, E, W, C, H, F, V, I, K, J, R, P, T
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 | 147 | 0.81 | 0.98 | 46 | MG, CAP, EDO |
| 2 | 147 | 0.81 | 0.98 | 45 | MG, CAP, EDO |
| 3 | 140 | 0.80 | 0.98 | 45 | MG, CAP, EDO |
| 4 | 148 | 0.80 | 0.97 | 46 | CAP, EDO |
| 5 | 895 | 0.78 | 0.81 | 64 | empty |
Interfaces
48 interfaces between chains.
- K–R · 4839 Ų buried · 93 hydrogen bonds · protein-protein
- H–V · 4829 Ų buried · 93 hydrogen bonds · protein-protein
- A–O · 4824 Ų buried · 89 hydrogen bonds · protein-protein
- B–E · 4820 Ų buried · 91 hydrogen bonds · protein-protein
- H–J · 2009 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 modified, 12 disulfide (hydroxylation, methylation, disulfide, carboxylation).
Compared structures
- 1UWA · L290F mutant rubisco from chlamydomonas · 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 P00877
- Every structure of UniProt P00873
- Elsewhere: RCSB PDB 1UWA · PDBe 1UWA · UniProt P00877 · UniProt P00873
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