Research workbench
Crystal structure of APC86534.1 (C-terminal domain of ncbi AAB90184.1; pfam big 123.1)
Analyse Crystal structure of APC86534.1 (C-terminal domain of ncbi AAB90184.1; pfam big… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QMM
- Type
- protein
- Length
- 390 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- UPF0217 protein AF_1056
- UniProt
- O29206
- Ligands
- SAM
- Pockets
- 3 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | UPF0217 protein AF_1056 | protein | 195 | 32% helix, 27% strand | O29206 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 154 | 0.61 | 0.84 | 31 | SAM |
| 2 | 158 | 0.60 | 0.83 | 35 | SAM |
| 3 | 58 | 0.29 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1521 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 2QMM · Crystal structure of APC86534.1 (C-terminal domain of NCBI AAB90184.1; Pfam BIG 123.1) · the same entry in another collection · chain A against A, TM-score 1.00
- O29206 · AlphaFold monomer V2.0 prediction for tRNA (PSEUDOURIDINE(54)-N(1))-methyltransferase… · a predicted model of the same protein · 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 O29206
- Elsewhere: RCSB PDB 2QMM · PDBe 2QMM · UniProt O29206
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