Research workbench
Crystal structure of the ACVRL1 (ALK1) kinase domain bound to ldn- 193189
Analyse Crystal structure of the ACVRL1 (ALK1) kinase domain bound to ldn- 193189 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MY0
- Type
- protein
- Length
- 6,930 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase receptor R3
- EC
- 2.7.11.30
- UniProt
- P37023
- Ligands
- LDN
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 18 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, L | SERINE/THREONINE-protein kinase receptor R3 (EC 2.7.11.30) | protein | 296 | 36% helix, 20% strand | P37023 |
| B | SERINE/THREONINE-protein kinase receptor R3 (EC 2.7.11.30) | protein | 295 | 38% helix, 20% strand | P37023 |
| C | SERINE/THREONINE-protein kinase receptor R3 (EC 2.7.11.30) | protein | 299 | 38% helix, 20% strand | P37023 |
| D | SERINE/THREONINE-protein kinase receptor R3 (EC 2.7.11.30) | protein | 298 | 38% helix, 19% strand | P37023 |
| E, F, G, Q, R | SERINE/THREONINE-protein kinase receptor R3 (EC 2.7.11.30) | protein | 294 | 41% helix, 19% strand | P37023 |
| H, S | SERINE/THREONINE-protein kinase receptor R3 (EC 2.7.11.30) | protein | 294 | 37% helix, 20% strand | P37023 |
| I | SERINE/THREONINE-protein kinase receptor R3 (EC 2.7.11.30) | protein | 293 | 41% helix, 19% strand | P37023 |
| J | SERINE/THREONINE-protein kinase receptor R3 (EC 2.7.11.30) | protein | 252 | 40% helix, 18% strand | P37023 |
| K | SERINE/THREONINE-protein kinase receptor R3 (EC 2.7.11.30) | protein | 261 | 39% helix, 17% strand | P37023 |
| M | SERINE/THREONINE-protein kinase receptor R3 (EC 2.7.11.30) | protein | 298 | 39% helix, 20% strand | P37023 |
| N | SERINE/THREONINE-protein kinase receptor R3 (EC 2.7.11.30) | protein | 300 | 37% helix, 20% strand | P37023 |
| O | SERINE/THREONINE-protein kinase receptor R3 (EC 2.7.11.30) | protein | 297 | 39% helix, 20% strand | P37023 |
| P | SERINE/THREONINE-protein kinase receptor R3 (EC 2.7.11.30) | protein | 290 | 37% helix, 17% strand | P37023 |
| T | SERINE/THREONINE-protein kinase receptor R3 (EC 2.7.11.30) | protein | 292 | 39% helix, 20% strand | P37023 |
| U | SERINE/THREONINE-protein kinase receptor R3 (EC 2.7.11.30) | protein | 285 | 42% helix, 19% strand | P37023 |
| V | SERINE/THREONINE-protein kinase receptor R3 (EC 2.7.11.30) | protein | 282 | 40% helix, 17% strand | P37023 |
| W | SERINE/THREONINE-protein kinase receptor R3 (EC 2.7.11.30) | protein | 281 | 39% helix, 18% strand | P37023 |
| X | SERINE/THREONINE-protein kinase receptor R3 (EC 2.7.11.30) | protein | 257 | 40% helix, 18% strand | P37023 |
Ligands and binding sites
- LDN · 4-[6-(4-piperazin-1-ylphenyl)pyrazolo[1,5-a]pyrimidin-3-yl]quinoline · ligand · 24 copies · chains A, F, B, C, D, E, G, H, I, J, K, L, Q, M, N, O, P, R, S, T, U, V, W, X
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 | 927 | 0.82 | 0.84 | 107 | LDN |
| 2 | 1065 | 0.81 | 0.82 | 86 | empty |
| 3 | 735 | 0.81 | 0.85 | 67 | empty |
| 4 | 889 | 0.81 | 0.83 | 93 | empty |
| 5 | 1023 | 0.81 | 0.82 | 102 | empty |
Interfaces
44 interfaces between chains.
- R–T · 856 Ų buried · 12 hydrogen bonds · protein-protein
- G–I · 834 Ų buried · 12 hydrogen bonds · protein-protein
- M–Q · 786 Ų buried · 11 hydrogen bonds · protein-protein
- O–T · 786 Ų buried · 13 hydrogen bonds · protein-protein
- D–I · 772 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3MY0 · Crystal structure of the ACVRL1 (ALK1) kinase domain bound to LDN-193189 · the same entry in another collection · chain E against E, 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 P37023
- Elsewhere: RCSB PDB 3MY0 · PDBe 3MY0 · UniProt P37023
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