MolNFT v1 · #14324 · protein
Crystal structure of a novel sm-like archaeal protein from pyrobaculum aerophilum
1M5Q · Small nuclear ribonucleoprotein homolog: “Crystal structure of a novel sm-like archaeal protein from pyrobaculum aerophilum”. X-ray diffraction, 2 ligands (CD, NA), 20 pockets (best druggability 0.81). MolNFT v1 #14324 on GenesisL1…
- PDB
- 1M5Q
- Type
- protein
- Length
- 3,566 residues
- Chains
- 28
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Small nuclear ribonucleoprotein homolog
- UniProt
- Q8ZVU2
- Ligands
- CD, NA
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Small nuclear ribonucleoprotein homolog | protein | 126 | 26% helix, 40% strand | Q8ZVU2 |
| B, C, D, E, F, G, L, O, P, Q, R, S, T, U, 1, 2 | Small nuclear ribonucleoprotein homolog | protein | 127 | 26% helix, 40% strand | Q8ZVU2 |
| H, I, J, K, M, N, V, W, X, Y, Z | Small nuclear ribonucleoprotein homolog | protein | 128 | 27% helix, 39% strand | Q8ZVU2 |
Ligands and binding sites
- CD · Cadmium ion · metal · 28 copies · chains A, B, G, C, D, E, F, H, I, N, J, K, L, M, O, U, P, Q, R, S, T, V, W, X, Y, Z, 1, 2
- NA · Sodium ion · metal · 5 copies · chains A, G, B, C, Q, R, S, V, W
- ACY · Acetic acid · additive · 15 copies · chains F, G, A, H, I, E, K, C, M, B, N, Q, V, P, W, O, X, U, Y, T, Z, S, 1, R, 2
- GOL · Glycerol · additive · 12 copies · chains A, B, G, H, I, J, K, M, N, R, 1, 2, P, V, W, X, O
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 | 1050 | 0.81 | 0.83 | 90 | CD, GOL |
| 2 | 924 | 0.80 | 0.82 | 76 | CD |
| 3 | 801 | 0.79 | 0.83 | 73 | CD |
| 4 | 879 | 0.79 | 0.82 | 71 | CD |
| 5 | 634 | 0.79 | 0.85 | 67 | GOL, CD |
Interfaces
75 interfaces between chains.
- P–V · 1124 Ų buried · 14 hydrogen bonds · protein-protein
- B–M · 1107 Ų buried · 14 hydrogen bonds · protein-protein
- D–K · 1098 Ų buried · 17 hydrogen bonds · protein-protein
- U–X · 1092 Ų buried · 21 hydrogen bonds · protein-protein
- E–J · 1089 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 84 modified (engineered).
Compared structures
- 1M5Q · Crystal structure of a novel Sm-like archaeal protein from Pyrobaculum aerophilum · 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 Q8ZVU2
- Elsewhere: RCSB PDB 1M5Q · PDBe 1M5Q · UniProt Q8ZVU2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.