Research workbench
Crystal structure of human menin in complex with MLL1 and ledgf
Analyse Crystal structure of human menin in complex with MLL1 and ledgf in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3U88
- Type
- protein
- Length
- 1,222 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Menin; Histone-lysine N-methyltransferase 2A; Lens epithelium-derived growth factor
- EC
- 2.1.1.43
- UniProt
- O00255, Q03164, O75475
- Ligands
- GLV, GGB, CHD, 0BR, SO4
- Pockets
- 16 · best druggability 0.82
Structure
x-ray diffraction · 6 distinct chains · 55% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Menin | protein | 477 | 53% helix, 8% strand | O00255 |
| B | Menin | protein | 485 | 53% helix, 8% strand | O00255 |
| M | Histone-lysine N-methyltransferase 2A (EC 2.1.1.43) | protein | 56 | 45% helix, 9% strand | Q03164 |
| C | Lens epithelium-derived growth factor | protein | 82 | 71% helix, 2% strand | O75475 |
| N | Histone-lysine N-methyltransferase 2A (EC 2.1.1.43) | protein | 55 | 42% helix, 9% strand | Q03164 |
| D | Lens epithelium-derived growth factor | protein | 67 | 78% helix, 0% strand | O75475 |
Ligands and binding sites
- GLV · Glyoxylic acid · ligand · 6 copies · chains A, M, B, N, C, D
- GGB · L-canavanine · ligand · 5 copies · chains A, B, C
- CHD · Cholic acid · ligand · 2 copies · chains A, B
- 0BR · (4beta,8alpha,9R)-6'-methoxy-10,11-dihydrocinchonan-9-ol · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, M, C, N, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 736 | 0.82 | 0.85 | 67 | GLV, SO4 |
| 2 | 579 | 0.79 | 0.85 | 46 | SO4 |
| 3 | 872 | 0.77 | 0.80 | 62 | 0BR |
| 4 | 391 | 0.61 | 0.77 | 54 | GGB, SO4, GLV |
| 5 | 103 | 0.59 | 0.87 | 22 | GLV |
Interfaces
9 interfaces between chains.
- A–M · 2534 Ų buried · 38 hydrogen bonds · protein-protein
- B–N · 2433 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 497 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 492 Ų buried · 3 hydrogen bonds · protein-protein
- M–C · 403 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3U88 · Crystal structure of human menin in complex with MLL1 and LEDGF · the same entry in another collection · chain D against D, TM-score 1.00
- O00255 · AlphaFold monomer V2.0 prediction for menin (O00255) · a predicted model of the same protein · chain A against A, TM-score 0.99
- O75475 · AlphaFold monomer V2.0 prediction for PC4 and SFRS1-interacting protein (O75475) · a predicted model of the same protein · chain C against A, TM-score 0.97
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 O00255
- Every structure of UniProt Q03164
- Every structure of UniProt O75475
- Elsewhere: RCSB PDB 3U88 · PDBe 3U88 · UniProt O00255 · UniProt Q03164 · UniProt O75475
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