Research workbench
Cryo-EM structure of ncp-6-4PP
Analyse Cryo-EM structure of ncp-6-4PP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6R93
- Type
- protein + DNA
- Length
- 1,065 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 a 6-4PP at…
- UniProt
- P68431, P62805, P04908, P06899
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 7 distinct chains · 61% 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 a 6-4PP at positions 95-96 | dna | 145 | — | — |
| A, E | Histone H3.1 | protein | 99 | 67% helix, 4% strand | P68431 |
| B, F | Histone H4 | protein | 82 | 60% helix, 9% strand | P62805 |
| C | Histone H2A type 1-B/E | protein | 111 | 53% helix, 6% strand | P04908 |
| D, H | Histone H2B type 1-J | protein | 97 | 72% helix, 4% strand | P06899 |
| G | Histone H2A type 1-B/E | protein | 108 | 55% helix, 6% strand | P04908 |
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 506 | 0.79 | 0.86 | 50 | empty |
| 2 | 463 | 0.77 | 0.85 | 56 | empty |
| 3 | 472 | 0.74 | 0.83 | 43 | empty |
| 4 | 149 | 0.71 | 0.91 | 29 | empty |
| 5 | 729 | 0.71 | 0.78 | 53 | empty |
Interfaces
36 interfaces between chains.
- I–J · 6343 Ų buried · 425 hydrogen bonds · nucleic-nucleic
- E–F · 2595 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 2556 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 2547 Ų buried · 9 hydrogen bonds · protein-protein
- G–H · 2546 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6R93 · Cryo-EM structure of NCP-6-4PP · 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 6R93 · PDBe 6R93 · UniProt P68431 · UniProt P62805 · UniProt P04908 · UniProt P06899
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