Research workbench
Structure of the K. lactis CBF3 core - NDC10 D1D2 complex
Analyse Structure of the K. lactis CBF3 core - NDC10 D1D2 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6P7X
- Type
- protein
- Length
- 1,833 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NDC10; CTF13; SKP1; CEP3
- UniProt
- Q6CPM4, Q6CK37, O94228, Q6CRD4
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 5 distinct chains · 56% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | NDC10 | protein | 385 | 50% helix, 6% strand | Q6CPM4 |
| C | CTF13 | protein | 387 | 27% helix, 17% strand | Q6CK37 |
| D | SKP1 | protein | 126 | 55% helix, 13% strand | O94228 |
| B | CEP3 | protein | 476 | 71% helix, 0% strand | Q6CRD4 |
| A | CEP3 | protein | 459 | 72% helix, 0% strand | Q6CRD4 |
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 | 560 | 0.84 | 0.89 | 75 | empty |
| 2 | 884 | 0.82 | 0.84 | 90 | empty |
| 3 | 747 | 0.80 | 0.84 | 72 | empty |
| 4 | 119 | 0.78 | 0.95 | 31 | empty |
| 5 | 244 | 0.75 | 0.88 | 38 | empty |
Interfaces
5 interfaces between chains.
- B–A · 1474 Ų buried · 10 hydrogen bonds · protein-protein
- C–B · 1348 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1066 Ų buried · 4 hydrogen bonds · protein-protein
- E–C · 818 Ų buried · 7 hydrogen bonds · protein-protein
- D–B · 319 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6P7X · Structure of the K. lactis CBF3 core - Ndc10 D1D2 complex · 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 Q6CPM4
- Every structure of UniProt Q6CK37
- Every structure of UniProt O94228
- Every structure of UniProt Q6CRD4
- Elsewhere: RCSB PDB 6P7X · PDBe 6P7X · UniProt Q6CPM4 · UniProt Q6CK37 · UniProt O94228 · UniProt Q6CRD4
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