MolNFT v1 · #188671 · protein + DNA
Cryoem structure of cenp-N promoted nucleosome stacks with cenp-a and 601 DNA sequence
7U4D · Histone H3-like centromeric protein a: “Cryoem structure of cenp-N promoted nucleosome stacks with cenp-a and 601 DNA sequence”. Electron microscopy, 20 pockets (best druggability 0.83). MolNFT v1 #188671 on GenesisL1: 3D structure…
- PDB
- 7U4D
- Type
- protein + DNA
- Length
- 2,406 residues
- Chains
- 22
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3-like centromeric protein a; Histone H4; Histone H2A; Histone H2B type…
- UniProt
- P49450, P62805, Q93077, P62807, Q96H22
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 10 distinct chains · 55% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, L | Histone H3-like centromeric protein a | protein | 89 | 53% helix, 4% strand | P49450 |
| B, M | Histone H4 | protein | 79 | 58% helix, 8% strand | P62805 |
| C, N | Histone H2A | protein | 99 | 57% helix, 4% strand | Q93077 |
| D, H, O, S | Histone H2B type 1-C/E/F/G/I | protein | 92 | 66% helix, 2% strand | P62807 |
| E, P | Histone H3-like centromeric protein a | protein | 91 | 64% helix, 3% strand | P49450 |
| F, Q | Histone H4 | protein | 78 | 60% helix, 6% strand | P62805 |
| G, R | Histone H2A | protein | 100 | 53% helix, 6% strand | Q93077 |
| I, T | DNA (147-mer) | dna | 139 | — | — |
| J, U | DNA (147-mer) | dna | 139 | — | — |
| K, V | Centromere protein N | protein | 205 | 43% helix, 19% strand | Q96H22 |
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 | 845 | 0.83 | 0.86 | 109 | empty |
| 2 | 963 | 0.83 | 0.85 | 75 | empty |
| 3 | 1048 | 0.82 | 0.83 | 105 | empty |
| 4 | 597 | 0.81 | 0.87 | 66 | empty |
| 5 | 921 | 0.81 | 0.83 | 89 | empty |
Interfaces
92 interfaces between chains.
- T–U · 6341 Ų buried · 527 hydrogen bonds · nucleic-nucleic
- I–J · 6333 Ų buried · 527 hydrogen bonds · nucleic-nucleic
- C–D · 2542 Ų buried · 21 hydrogen bonds · protein-protein
- N–O · 2535 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 2523 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 7U4D · CryoEM structure of CENP-N promoted nucleosome stacks with CENP-A and 601 DNA sequence · the same entry in another collection · chain K against K, 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 P49450
- Every structure of UniProt P62805
- Every structure of UniProt Q93077
- Every structure of UniProt P62807
- Every structure of UniProt Q96H22
- Elsewhere: RCSB PDB 7U4D · PDBe 7U4D · UniProt P49450 · UniProt P62805 · UniProt Q93077 · UniProt P62807 · UniProt Q96H22
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