MolNFT v1 · #117989 · protein
Structure of full-length human MAB21L1 with bound CTP
5EOM · Protein mab-21-like 1: “Structure of full-length human MAB21L1 with bound CTP”. X-ray diffraction, 2 ligands (CTP, TMO), 20 pockets (best druggability 0.78). MolNFT v1 #117989 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5EOM
- Type
- protein
- Length
- 3,409 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein mab-21-like 1
- UniProt
- Q13394
- Ligands
- CTP, TMO
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 10 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein mab-21-like 1 | protein | 349 | 48% helix, 15% strand | Q13394 |
| B | Protein mab-21-like 1 | protein | 349 | 49% helix, 16% strand | Q13394 |
| D | Protein mab-21-like 1 | protein | 342 | 51% helix, 16% strand | Q13394 |
| E | Protein mab-21-like 1 | protein | 348 | 49% helix, 16% strand | Q13394 |
| F | Protein mab-21-like 1 | protein | 339 | 50% helix, 15% strand | Q13394 |
| G | Protein mab-21-like 1 | protein | 352 | 49% helix, 17% strand | Q13394 |
| H | Protein mab-21-like 1 | protein | 345 | 50% helix, 17% strand | Q13394 |
| I | Protein mab-21-like 1 | protein | 346 | 51% helix, 15% strand | Q13394 |
| J | Protein mab-21-like 1 | protein | 286 | 49% helix, 11% strand | Q13394 |
| C | Protein mab-21-like 1 | protein | 353 | 49% helix, 16% strand | Q13394 |
Ligands and binding sites
- CTP · Cytidine-5'-triphosphate · ligand · 10 copies · chains A, B, D, E, F, G, H, I, J, C
- TMO · trimethylamine oxide · ligand · 4 copies · chains A, F, C
- CIT · Citric acid · additive · 10 copies · chains A, D, B, C, F, E, G, I, H, J
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 | 920 | 0.78 | 0.81 | 63 | CTP |
| 2 | 733 | 0.77 | 0.82 | 54 | empty |
| 3 | 965 | 0.77 | 0.79 | 62 | CTP |
| 4 | 977 | 0.77 | 0.79 | 86 | CTP |
| 5 | 854 | 0.76 | 0.80 | 63 | CTP |
Interfaces
16 interfaces between chains.
- E–C · 1337 Ų buried · 20 hydrogen bonds · protein-protein
- B–G · 1199 Ų buried · 10 hydrogen bonds · protein-protein
- A–H · 1006 Ų buried · 4 hydrogen bonds · protein-protein
- F–I · 964 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 650 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5EOM · Structure of full-length human MAB21L1 with bound CTP · the same entry in another collection · chain C against C, TM-score 1.00
- Q13394 · AlphaFold monomer V2.0 prediction for putative nucleotidyltransferase MAB21L1 (Q13394) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q13394
- Elsewhere: RCSB PDB 5EOM · PDBe 5EOM · UniProt Q13394
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