MolNFT v1 · #124061 · protein
Crystal structure of AURORAB/INCENP in complex with bi 811283
5K3Y · Aurora kinase B-a: “Crystal structure of AURORAB/INCENP in complex with bi 811283”. X-ray diffraction, 2 ligands (TPO, 6Q4), 7 pockets (best druggability 0.74). MolNFT v1 #124061 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5K3Y
- Type
- protein
- Length
- 615 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aurora kinase B-a; Inner centromere protein a
- EC
- 2.7.11.1
- UniProt
- Q6DE08, O13024
- Ligands
- TPO, 6Q4
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aurora kinase B-a (EC 2.7.11.1) | protein | 267 | 40% helix, 19% strand | Q6DE08 |
| B | Aurora kinase B-a (EC 2.7.11.1) | protein | 277 | 39% helix, 19% strand | Q6DE08 |
| C | Inner centromere protein a | protein | 35 | 57% helix, 0% strand | O13024 |
| D | Inner centromere protein a | protein | 36 | 56% helix, 0% strand | O13024 |
Ligands and binding sites
- TPO · Phosphothreonine · ligand · 2 copies · chains A, B
- 6Q4 · N-methyl-N-(1-methylpiperidin-4-yl)-4-{[4-({(1R,2S)-2-[(propan-2-yl)carbamoyl]cyclopentyl}amino)-5-(trifluoromethyl)pyrimidin-2-yl]amino}benzamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 299 | 0.74 | 0.86 | 28 | empty |
| 2 | 299 | 0.72 | 0.85 | 32 | empty |
| 3 | 323 | 0.70 | 0.83 | 41 | 6Q4 |
| 4 | 288 | 0.65 | 0.81 | 40 | 6Q4 |
| 5 | 61 | 0.31 | 0.76 | 13 | empty |
Interfaces
2 interfaces between chains.
- B–C · 1780 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 1583 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 5K3Y · Crystal structure of AuroraB/INCENP in complex with BI 811283 · the same entry in another collection · chain B against B, TM-score 1.00
- Q6DE08 · AlphaFold monomer V2.0 prediction for aurora kinase B-a (Q6DE08) · a predicted model of the same protein · chain A against A, TM-score 0.99
- O13024 · AlphaFold monomer V2.0 prediction for inner centromere protein a (O13024) · a predicted model of the same protein · chain D against A, TM-score 0.49
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 Q6DE08
- Every structure of UniProt O13024
- Elsewhere: RCSB PDB 5K3Y · PDBe 5K3Y · UniProt Q6DE08 · UniProt O13024
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