Research workbench
Structure of gamma-tubulin small complex based on a cryo-EM MAP, chemical cross-links, and a remotely related structure
Analyse Structure of gamma-tubulin small complex based on a cryo-EM MAP, chemical… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FM1
- Type
- protein
- Length
- 2,118 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spindle pole body component SPC97; Spindle pole body component SPC98; Tubulin gamma…
- UniProt
- P38863, P53540, P53378
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 4 distinct chains · 64% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spindle pole body component SPC97 | protein | 575 | 72% helix, 3% strand | P38863 |
| B | Spindle pole body component SPC98 | protein | 565 | 70% helix, 3% strand | P53540 |
| C, D | Tubulin gamma chain | protein | 445 | 42% helix, 18% strand | P53378 |
| E, F | Spindle pole body component 110 | protein | 44 | 95% helix, 0% strand | — |
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 151 | 0.82 | 0.97 | 25 | empty |
| 2 | 1117 | 0.82 | 0.83 | 95 | empty |
| 3 | 108 | 0.79 | 0.97 | 22 | empty |
| 4 | 119 | 0.78 | 0.97 | 29 | empty |
| 5 | 146 | 0.76 | 0.92 | 26 | empty |
Interfaces
9 interfaces between chains.
- B–D · 2735 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 2712 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1527 Ų buried · 39 hydrogen bonds · protein-protein
- B–E · 390 Ų buried · 3 hydrogen bonds · protein-protein
- A–F · 302 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5FM1 · Structure of gamma-tubulin small complex based on a cryo-EM map, chemical cross-links… · the same entry in another collection · chain F against F, TM-score 1.00
- P53378 · AlphaFold monomer V2.0 prediction for tubulin gamma chain (P53378) · a predicted model of the same protein · chain C against A, TM-score 0.91
- P53540 · AlphaFold monomer V2.0 prediction for spindle pole body component SPC98 (P53540) · a predicted model of the same protein · chain B against A, TM-score 0.88
- P38863 · AlphaFold monomer V2.0 prediction for spindle pole body component SPC97 (P38863) · a predicted model of the same protein · chain A against A, TM-score 0.85
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 P38863
- Every structure of UniProt P53540
- Every structure of UniProt P53378
- Elsewhere: RCSB PDB 5FM1 · PDBe 5FM1 · UniProt P38863 · UniProt P53540 · UniProt P53378
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