Research workbench
Cryo-EM structure of NCP_THF2(-3)
Analyse Cryo-EM structure of NCP_THF2(-3) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6R94
- Type
- protein + DNA
- Length
- 1,093 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Human alpha-satellite DNA (145-mer); Human alpha-satellite DNA (145-mer) with abasic…
- UniProt
- P68431, P62805, P04908, P06899
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 9 distinct chains · 60% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I | Human alpha-satellite DNA (145-mer) | dna | 145 | — | — |
| J | Human alpha-satellite DNA (145-mer) with abasic sites at positions 97-98 | dna | 145 | — | — |
| A, E | Histone H3.1 | protein | 101 | 62% helix, 4% strand | P68431 |
| B | Histone H4 | protein | 84 | 60% helix, 8% strand | P62805 |
| C | Histone H2A type 1-B/E | protein | 115 | 50% helix, 6% strand | P04908 |
| D | Histone H2B type 1-J | protein | 97 | 72% helix, 4% strand | P06899 |
| F | Histone H4 | protein | 87 | 56% helix, 8% strand | P62805 |
| G | Histone H2A type 1-B/E | protein | 118 | 50% helix, 6% strand | P04908 |
| H | Histone H2B type 1-J | protein | 100 | 70% helix, 4% strand | P06899 |
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 | 1095 | 0.82 | 0.83 | 130 | empty |
| 2 | 369 | 0.76 | 0.87 | 47 | empty |
| 3 | 163 | 0.70 | 0.90 | 25 | empty |
| 4 | 657 | 0.70 | 0.79 | 54 | empty |
| 5 | 751 | 0.70 | 0.77 | 45 | empty |
Interfaces
37 interfaces between chains.
- I–J · 6286 Ų buried · 468 hydrogen bonds · nucleic-nucleic
- A–B · 2802 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 2771 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 2622 Ų buried · 14 hydrogen bonds · protein-protein
- G–H · 2582 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 6R94 · Cryo-EM structure of NCP_THF2(-3) · the same entry in another collection · chain I against I, 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 P68431
- Every structure of UniProt P62805
- Every structure of UniProt P04908
- Every structure of UniProt P06899
- Elsewhere: RCSB PDB 6R94 · PDBe 6R94 · UniProt P68431 · UniProt P62805 · UniProt P04908 · UniProt P06899
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