Research workbench
GDP-microtubule complexed with KIF5C in amppnp state
Analyse GDP-microtubule complexed with KIF5C in amppnp state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XXV
- Type
- protein
- Length
- 7,686 residues
- Chains
- 18
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1A chain; Tubulin beta chain
- UniProt
- P02550, P02554
- Ligands
- GTP, GDP, MG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 2 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K, M, O, Q | Tubulin alpha-1A chain | protein | 428 | 44% helix, 19% strand | P02550 |
| B, D, F, H, J, L, N, P, R | Tubulin beta chain | protein | 426 | 49% helix, 19% strand | P02554 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 9 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R
- GDP · Guanosine-5'-diphosphate · ligand · 9 copies · chains B, I, D, G, F, K, H, J, L, C, N, A, P, E, R
- MG · Magnesium ion · metal · 9 copies · chains A, C, E, G, H, I, J, K, L, M, N, O, P, Q, R
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 | 307 | 0.85 | 0.95 | 48 | MG, GTP |
| 2 | 305 | 0.84 | 0.95 | 53 | MG, GTP |
| 3 | 282 | 0.84 | 0.95 | 49 | MG, GTP |
| 4 | 292 | 0.84 | 0.95 | 47 | MG, GTP |
| 5 | 296 | 0.84 | 0.95 | 48 | MG, GTP |
Interfaces
27 interfaces between chains.
- K–L · 2164 Ų buried · 63 hydrogen bonds · protein-protein
- Q–R · 2158 Ų buried · 62 hydrogen bonds · protein-protein
- G–H · 2157 Ų buried · 62 hydrogen bonds · protein-protein
- I–J · 2155 Ų buried · 62 hydrogen bonds · protein-protein
- O–P · 2153 Ų buried · 62 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 covalent, 9 disulfide (covalent ligand, disulfide).
Compared structures
- 5XXV · GDP-microtubule complexed with KIF5C in AMPPNP state · the same entry in another collection · chain R against R, 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 P02550
- Every structure of UniProt P02554
- Elsewhere: RCSB PDB 5XXV · PDBe 5XXV · UniProt P02550 · UniProt P02554
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