Research workbench
Crystal structure of RIB7 from methanosarcina mazei
Analyse Crystal structure of RIB7 from methanosarcina mazei in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XUX
- Type
- protein
- Length
- 1,370 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Conserved protein
- UniProt
- Q8PYN5
- Ligands
- NAP
- Pockets
- 14 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Conserved protein | protein | 238 | 25% helix, 28% strand | Q8PYN5 |
| B | Conserved protein | protein | 224 | 28% helix, 29% strand | Q8PYN5 |
| C | Conserved protein | protein | 224 | 26% helix, 30% strand | Q8PYN5 |
| D, E | Conserved protein | protein | 223 | 28% helix, 29% strand | Q8PYN5 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · 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
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 496 | 0.72 | 0.81 | 49 | NAP |
| 2 | 507 | 0.71 | 0.81 | 49 | NAP |
| 3 | 593 | 0.71 | 0.79 | 51 | NAP |
| 4 | 541 | 0.71 | 0.80 | 53 | NAP |
| 5 | 460 | 0.71 | 0.81 | 48 | NAP |
Interfaces
5 interfaces between chains.
- A–B · 1887 Ų buried · 28 hydrogen bonds · protein-protein
- E–F · 1880 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1755 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 768 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 756 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5XUX · Crystal structure of Rib7 from Methanosarcina mazei · the same entry in another collection · chain A 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 Q8PYN5
- Elsewhere: RCSB PDB 5XUX · PDBe 5XUX · UniProt Q8PYN5
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