Research workbench
Saga dub module UBP8/SGF11/SUS1/SGF73 bound to ubiqitinated nucleosome
Analyse Saga dub module UBP8/SGF11/SUS1/SGF73 bound to ubiqitinated nucleosome in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZUX
- Type
- protein + DNA
- Length
- 5,242 residues
- Chains
- 40
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.2; Histone H4; Histone H2A type 1; Histone H2B 1.1; DNA (145-mer); Ubiquitin…
- EC
- 3.4.19.12
- UniProt
- P84233, P62799, P06897, P02281, P50102, Q6WNK7, A6ZWK1, P0CG47, P53165
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 25 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, K | Histone H3.2 | protein | 97 | 66% helix, 4% strand | P84233 |
| B, L | Histone H4 | protein | 83 | 60% helix, 8% strand | P62799 |
| C, M | Histone H2A type 1 | protein | 103 | 56% helix, 7% strand | P06897 |
| D, N | Histone H2B 1.1 | protein | 95 | 74% helix, 4% strand | P02281 |
| E, O | Histone H3.2 | protein | 97 | 66% helix, 4% strand | P84233 |
| F, P | Histone H4 | protein | 78 | 67% helix, 9% strand | P62799 |
| G, Q | Histone H2A type 1 | protein | 105 | 56% helix, 7% strand | P06897 |
| H, R | Histone H2B 1.1 | protein | 93 | 75% helix, 4% strand | P02281 |
| I, S | DNA (145-mer) | dna | 145 | — | — |
| J, T | DNA (145-mer) | dna | 145 | — | — |
| U | Ubiquitin carboxyl-terminal hydrolase 8 (EC 3.4.19.12) | protein | 447 | 33% helix, 26% strand | P50102 |
| V | Transcription and mRNA export factor SUS1 | protein | 89 | 85% helix, 0% strand | Q6WNK7 |
| W, g | Saga-associated factor 11 | protein | 90 | 50% helix, 9% strand | A6ZWK1 |
| X, c, h, m | Polyubiquitin-B | protein | 76 | 20% helix, 33% strand | P0CG47 |
| Y | Saga-associated factor 73 | protein | 82 | 40% helix, 11% strand | P53165 |
| Z | Ubiquitin carboxyl-terminal hydrolase 8 (EC 3.4.19.12) | protein | 451 | 33% helix, 25% strand | P50102 |
| a | Transcription and mRNA export factor SUS1 | protein | 90 | 79% helix, 1% strand | Q6WNK7 |
| b | Saga-associated factor 11 | protein | 89 | 51% helix, 7% strand | A6ZWK1 |
| d, i | Saga-associated factor 73 | protein | 89 | 37% helix, 11% strand | P53165 |
| e | Ubiquitin carboxyl-terminal hydrolase 8 (EC 3.4.19.12) | protein | 453 | 34% helix, 26% strand | P50102 |
| f | Transcription and mRNA export factor SUS1 | protein | 85 | 79% helix, 1% strand | Q6WNK7 |
| j | Ubiquitin carboxyl-terminal hydrolase 8 (EC 3.4.19.12) | protein | 447 | 33% helix, 25% strand | P50102 |
| k | Transcription and mRNA export factor SUS1 | protein | 86 | 85% helix, 0% strand | Q6WNK7 |
| l | Saga-associated factor 11 | protein | 93 | 48% helix, 10% strand | A6ZWK1 |
| n | Saga-associated factor 73 | protein | 86 | 38% helix, 10% strand | P53165 |
Ligands and binding sites
- ZN · Zinc ion · metal · 32 copies · chains U, W, Y, Z, b, d, e, g, i, j, l, n
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 | 1053 | 0.87 | 0.88 | 102 | empty |
| 2 | 1146 | 0.87 | 0.88 | 112 | empty |
| 3 | 1193 | 0.86 | 0.87 | 124 | empty |
| 4 | 1118 | 0.86 | 0.87 | 100 | empty |
| 5 | 648 | 0.84 | 0.89 | 80 | empty |
Interfaces
139 interfaces between chains.
- S–T · 6756 Ų buried · 806 hydrogen bonds · nucleic-nucleic
- I–J · 6736 Ų buried · 783 hydrogen bonds · nucleic-nucleic
- Z–d · 3292 Ų buried · 39 hydrogen bonds · protein-protein
- U–Y · 3286 Ų buried · 35 hydrogen bonds · protein-protein
- e–i · 3273 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- P50102 · AlphaFold monomer V2.0 prediction for ubiquitin carboxyl-terminal hydrolase 8 (P50102) · a predicted model of the same protein · chain U against A, TM-score 0.99
- P06897 · AlphaFold monomer V2.0 prediction for histone H2A type 1 (P06897) · a predicted model of the same protein · chain C against A, TM-score 0.94
- Q6WNK7 · AlphaFold monomer V2.0 prediction for transcription and mRNA export factor SUS1 (Q6WNK7) · a predicted model of the same protein · chain k against A, TM-score 0.92
- P53165 · AlphaFold monomer V2.0 prediction for saga-associated factor 73 (P53165) · a predicted model of the same protein · chain n against A, TM-score 0.89
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 P84233
- Every structure of UniProt P62799
- Every structure of UniProt P06897
- Every structure of UniProt P02281
- Every structure of UniProt P50102
- Every structure of UniProt Q6WNK7
- Every structure of UniProt A6ZWK1
- Every structure of UniProt P0CG47
- Every structure of UniProt P53165
- Elsewhere: RCSB PDB 4ZUX · PDBe 4ZUX · UniProt P84233 · UniProt P62799 · UniProt P06897 · UniProt P02281 · UniProt P50102 · UniProt Q6WNK7 · UniProt A6ZWK1 · UniProt P0CG47 · UniProt P53165
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