Research workbench
Cryo-EM structure of the yeast pre-B complex at an average resolution of 3.3 ångström (part II: U1 snrnp region)
Analyse Cryo-EM structure of the yeast pre-B complex at an average resolution of 3.3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZWN
- Type
- protein + RNA
- Length
- 3,887 residues
- Chains
- 20
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pre-mRNA; U1 snrna; U1 small nuclear ribonucleoprotein 70 kda homolog; U1 small nuclear…
- EC
- 3.6.4.13
- UniProt
- Q00916, Q05900, P32605, Q03776, P39682, Q00539, Q03782, P40018, Q02260, Q06217, P43321, Q12330, P54999, P40204, P53207, Q07508, P23394
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 20 distinct chains · 42% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Pre-mRNA | rna | 22 | — | — |
| P | U1 snrna | rna | 480 | — | — |
| Q | U1 small nuclear ribonucleoprotein 70 kda homolog | protein | 186 | 35% helix, 17% strand | Q00916 |
| R | U1 small nuclear ribonucleoprotein C | protein | 184 | 41% helix, 5% strand | Q05900 |
| S | U1 small nuclear ribonucleoprotein a | protein | 131 | 36% helix, 11% strand | P32605 |
| T | U1 small nuclear ribonucleoprotein component PRP42 | protein | 539 | 72% helix, 0% strand | Q03776 |
| U | Pre-mRNA-processing factor 39 | protein | 583 | 62% helix, 1% strand | P39682 |
| V | Protein NAM8 | protein | 187 | 27% helix, 12% strand | Q00539 |
| W | 56 kda U1 small nuclear ribonucleoprotein component | protein | 229 | 49% helix, 20% strand | Q03782 |
| a | Small nuclear ribonucleoprotein-associated protein B | protein | 124 | 25% helix, 31% strand | P40018 |
| b | Small nuclear ribonucleoprotein sm D1 | protein | 119 | 24% helix, 31% strand | Q02260 |
| c | Small nuclear ribonucleoprotein sm D2 | protein | 101 | 21% helix, 45% strand | Q06217 |
| d | Small nuclear ribonucleoprotein sm D3 | protein | 92 | 21% helix, 41% strand | P43321 |
| e | Small nuclear ribonucleoprotein E | protein | 74 | 18% helix, 51% strand | Q12330 |
| f | Small nuclear ribonucleoprotein F | protein | 68 | 15% helix, 51% strand | P54999 |
| g | Small nuclear ribonucleoprotein G | protein | 75 | 4% helix, 45% strand | P40204 |
| X | U1 small nuclear ribonucleoprotein component SNU71 | protein | 49 | 47% helix, 20% strand | P53207 |
| Y | Protein LUC7 | protein | 196 | 65% helix, 2% strand | Q07508 |
| x | U1 snrnp | protein | 49 | 82% helix, 0% strand | — |
| y | Pre-mRNA-splicing ATP-dependent RNA helicase PRP28 (EC 3.6.4.13) | protein | 399 | 0% helix, 0% strand | P23394 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains R, Y
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 | 963 | 0.87 | 0.89 | 89 | empty |
| 2 | 643 | 0.84 | 0.89 | 98 | empty |
| 3 | 1036 | 0.83 | 0.84 | 81 | empty |
| 4 | 627 | 0.83 | 0.88 | 78 | empty |
| 5 | 1063 | 0.81 | 0.83 | 75 | empty |
Interfaces
63 interfaces between chains.
- T–U · 3713 Ų buried · 28 hydrogen bonds · protein-protein
- R–T · 2921 Ų buried · 30 hydrogen bonds · protein-protein
- P–R · 2389 Ų buried · 42 hydrogen bonds · protein-nucleic
- U–V · 2191 Ų buried · 16 hydrogen bonds · protein-protein
- T–W · 2168 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 5ZWN · Cryo-EM structure of the yeast pre-B complex at an average resolution of 3.3 angstrom… · the same entry in another collection · chain b against b, 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 Q00916
- Every structure of UniProt Q05900
- Every structure of UniProt P32605
- Every structure of UniProt Q03776
- Every structure of UniProt P39682
- Every structure of UniProt Q00539
- Every structure of UniProt Q03782
- Every structure of UniProt P40018
- Every structure of UniProt Q02260
- Every structure of UniProt Q06217
- Every structure of UniProt P43321
- Every structure of UniProt Q12330
- Every structure of UniProt P54999
- Every structure of UniProt P40204
- Every structure of UniProt P53207
- Every structure of UniProt Q07508
- Every structure of UniProt P23394
- Elsewhere: RCSB PDB 5ZWN · PDBe 5ZWN · UniProt Q00916 · UniProt Q05900 · UniProt P32605 · UniProt Q03776 · UniProt P39682 · UniProt Q00539 · UniProt Q03782 · UniProt P40018 · UniProt Q02260 · UniProt Q06217 · UniProt P43321 · UniProt Q12330 · UniProt P54999 · UniProt P40204 · UniProt P53207 · UniProt Q07508 · UniProt P23394
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