Research workbench
Crystal structure of Rhodospirillum rubrum Rru_A0973 mutant E62A
Analyse Crystal structure of Rhodospirillum rubrum Rru_A0973 mutant E62A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5L8B
- Type
- protein
- Length
- 2,675 residues
- Chains
- 30
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.21
- Source
- Rhodospirillum rubrum
- Molecule
- Uncharacterized protein
- UniProt
- Q2RVS1
- Ligands
- CA
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · resolution 2.21 · 7 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, M, N | Uncharacterized protein | protein | 90 | 77% helix, 0% strand | Q2RVS1 |
| B, C, D, G, H, L, P, T, c | Uncharacterized protein | protein | 89 | 78% helix, 0% strand | Q2RVS1 |
| E, I, J, Q, R, S, U | Uncharacterized protein | protein | 91 | 80% helix, 0% strand | Q2RVS1 |
| F, K, W, X, Y, Z, a, b | Uncharacterized protein | protein | 88 | 80% helix, 0% strand | Q2RVS1 |
| O | Uncharacterized protein | protein | 90 | 81% helix, 0% strand | Q2RVS1 |
| V | Uncharacterized protein | protein | 84 | 80% helix, 0% strand | Q2RVS1 |
| d | Uncharacterized protein | protein | 89 | 74% helix, 0% strand | Q2RVS1 |
Ligands and binding sites
- CA · Calcium ion · metal · 24 copies · chains A, J, B, C, D, E, F, H, G, I, O, K, T, L, M, N, P, R, Q, S, U, d, V, W, X, Y, Z, b, a, 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1010 | 0.79 | 0.81 | 100 | empty |
| 2 | 1199 | 0.74 | 0.78 | 73 | empty |
| 3 | 60 | 0.72 | 0.98 | 26 | empty |
| 4 | 67 | 0.71 | 0.97 | 23 | CA |
| 5 | 62 | 0.71 | 0.97 | 24 | empty |
Interfaces
75 interfaces between chains.
- Q–R · 2587 Ų buried · 47 hydrogen bonds · protein-protein
- C–D · 2574 Ų buried · 43 hydrogen bonds · protein-protein
- G–H · 2572 Ų buried · 48 hydrogen bonds · protein-protein
- c–d · 2557 Ų buried · 50 hydrogen bonds · protein-protein
- a–b · 2557 Ų buried · 43 hydrogen bonds · protein-protein
Compared structures
- 5L8B · Crystal structure of rhodospirillum rubrum RRU_A0973 mutant E62A · the same entry in another collection · chain B against B, 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 Q2RVS1
- Elsewhere: RCSB PDB 5L8B · PDBe 5L8B · UniProt Q2RVS1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.