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Crystal structure of a methanobacterial sm-like archaeal protein (SMAP1) bound to uridine-5'-monophosphate (ump)
Analyse Crystal structure of a methanobacterial sm-like archaeal protein (SMAP1) bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LOJ
- Type
- protein
- Length
- 1,047 residues
- Chains
- 14
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Small nuclear ribonucleoprotein homolog (sm- like)
- UniProt
- O26745
- Ligands
- URI, U
- Pockets
- 19 · best druggability 0.78
Structure
x-ray diffraction · 8 distinct chains · 16% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Small nuclear ribonucleoprotein homolog (sm- like) | protein | 76 | 18% helix, 55% strand | O26745 |
| B, J | Small nuclear ribonucleoprotein homolog (sm- like) | protein | 76 | 14% helix, 55% strand | O26745 |
| C | Small nuclear ribonucleoprotein homolog (sm- like) | protein | 77 | 14% helix, 55% strand | O26745 |
| D, I, L, N | Small nuclear ribonucleoprotein homolog (sm- like) | protein | 74 | 15% helix, 54% strand | O26745 |
| E, F, G | Small nuclear ribonucleoprotein homolog (sm- like) | protein | 75 | 15% helix, 56% strand | O26745 |
| H | Small nuclear ribonucleoprotein homolog (sm- like) | protein | 76 | 14% helix, 57% strand | O26745 |
| K | Small nuclear ribonucleoprotein homolog (sm- like) | protein | 72 | 15% helix, 57% strand | O26745 |
| M | Small nuclear ribonucleoprotein homolog (sm- like) | protein | 73 | 19% helix, 58% strand | O26745 |
Ligands and binding sites
- URI · Uridine · ligand · 8 copies · chains A, B, C, D, E, F, G, I, J, K, L, M, N
- U · Uridine-5'-monophosphate · ligand · 6 copies · chains A, B, G, C, D, E, H, I, N, J, K, L, M
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 14 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 731 | 0.78 | 0.83 | 75 | empty |
| 2 | 523 | 0.75 | 0.83 | 53 | empty |
| 3 | 345 | 0.70 | 0.83 | 35 | empty |
| 4 | 106 | 0.54 | 0.83 | 19 | MPD |
| 5 | 92 | 0.52 | 0.83 | 18 | MPD |
Interfaces
28 interfaces between chains.
- A–G · 924 Ų buried · 15 hydrogen bonds · protein-protein
- H–N · 918 Ų buried · 19 hydrogen bonds · protein-protein
- F–G · 896 Ų buried · 14 hydrogen bonds · protein-protein
- H–I · 893 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 868 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 1LOJ · Crystal structure of a Methanobacterial Sm-like archaeal protein (SmAP1) bound to… · the same entry in another collection · chain N against N, 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 O26745
- Elsewhere: RCSB PDB 1LOJ · PDBe 1LOJ · UniProt O26745
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