MolNFT v1 · #156106 · protein + DNA
Structure of nucleosome-bound human baf complex
6LTJ · Histone H3.3: “Structure of nucleosome-bound human baf complex”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.86). MolNFT v1 #156106 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6LTJ
- Type
- protein + DNA
- Length
- 3,894 residues
- Chains
- 20
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.3; Histone H4; Histone H2A type 1; Histone H2B; Transcription activator BRG1…
- EC
- 3.6.4.-
- UniProt
- Q6PI79, P62799, P06897, Q92131, P51532, O96019, P60709, O14497, Q12824, Q8TAQ2, Q96GM5, Q969G3, Q92785
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 19 distinct chains · 55% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Histone H3.3 | protein | 91 | 70% helix, 4% strand | Q6PI79 |
| B | Histone H4 | protein | 78 | 65% helix, 8% strand | P62799 |
| C | Histone H2A type 1 | protein | 95 | 56% helix, 6% strand | P06897 |
| D | Histone H2B | protein | 88 | 76% helix, 5% strand | Q92131 |
| F | Histone H4 | protein | 77 | 64% helix, 8% strand | P62799 |
| G | Histone H2A type 1 | protein | 95 | 60% helix, 6% strand | P06897 |
| H | Histone H2B | protein | 90 | 71% helix, 4% strand | Q92131 |
| I | Transcription activator BRG1 (EC 3.6.4.-) | protein | 551 | 49% helix, 3% strand | P51532 |
| J | Actin-like protein 6A | protein | 334 | 36% helix, 19% strand | O96019 |
| K | Actin, cytoplasmic 1 | protein | 317 | 43% helix, 15% strand | P60709 |
| L | At-rich interactive domain-containing protein 1A | protein | 466 | 55% helix, 2% strand | O14497 |
| M | SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 | protein | 283 | 44% helix, 20% strand | Q12824 |
| N | SWI/SNF complex subunit SMARCC2 | protein | 261 | 74% helix, 2% strand | Q8TAQ2 |
| O | SWI/SNF complex subunit SMARCC2 | protein | 325 | 62% helix, 3% strand | Q8TAQ2 |
| P | SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 | protein | 239 | 65% helix, 5% strand | Q96GM5 |
| Q | SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 | protein | 105 | 71% helix, 0% strand | Q969G3 |
| R | Zinc finger protein ubi-D4 | protein | 70 | 39% helix, 17% strand | Q92785 |
| X | DNA (119-mer) | dna | 119 | — | — |
| Y | DNA (119-mer) | dna | 119 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · chains L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 1000 | 0.86 | 0.87 | 127 | empty |
| 2 | 742 | 0.84 | 0.87 | 83 | empty |
| 3 | 696 | 0.83 | 0.86 | 58 | empty |
| 4 | 958 | 0.83 | 0.84 | 100 | empty |
| 5 | 1162 | 0.81 | 0.83 | 94 | empty |
Interfaces
67 interfaces between chains.
- X–Y · 5347 Ų buried · 429 hydrogen bonds · nucleic-nucleic
- N–O · 2958 Ų buried · 17 hydrogen bonds · protein-protein
- O–P · 2588 Ų buried · 17 hydrogen bonds · protein-protein
- G–H · 2580 Ų buried · 19 hydrogen bonds · protein-protein
- L–P · 2520 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 6LTJ · Structure of nucleosome-bound human BAF complex · the same entry in another collection · chain J against J, 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 Q6PI79
- Every structure of UniProt P62799
- Every structure of UniProt P06897
- Every structure of UniProt Q92131
- Every structure of UniProt P51532
- Every structure of UniProt O96019
- Every structure of UniProt P60709
- Every structure of UniProt O14497
- Every structure of UniProt Q12824
- Every structure of UniProt Q8TAQ2
- Every structure of UniProt Q96GM5
- Every structure of UniProt Q969G3
- Every structure of UniProt Q92785
- Elsewhere: RCSB PDB 6LTJ · PDBe 6LTJ · UniProt Q6PI79 · UniProt P62799 · UniProt P06897 · UniProt Q92131 · UniProt P51532 · UniProt O96019 · UniProt P60709 · UniProt O14497 · UniProt Q12824 · UniProt Q8TAQ2 · UniProt Q96GM5 · UniProt Q969G3 · UniProt Q92785
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