MolNFT v1 · #172315 · protein + RNA
Human C complex spliceosome - high-resolution core
6ZYM · U2 snrna: “Human C complex spliceosome - high-resolution core”. Electron microscopy, 4 ligands (IHP, GTP, ZN), 20 pockets (best druggability 0.89). MolNFT v1 #172315 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6ZYM
- Type
- protein + RNA
- Length
- 5,678 residues
- Chains
- 26
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- U2 snrna; U5 snrna; U6 snrna; Corepressor interacting with rbpj 1…
- EC
- 5.2.1.8, 3.6.4.13
- UniProt
- Q86X95, Q6P2Q9, Q15029, Q13573, O43660, O60508, Q96DI7, Q99459, Q9BZJ0, Q9NW64, P41223, Q9P013, Q9UQ35, Q9HCG8, Q9Y3C6, Q9NW82, Q92620, Q9ULR0, Q9NXE8, Q9BW85, Q14331
- Ligands
- IHP, GTP, ZN, MG
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 26 distinct chains · 32% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 2 | U2 snrna | rna | 27 | — | — |
| 5 | U5 snrna | rna | 74 | — | — |
| 6 | U6 snrna | rna | 79 | — | — |
| 9 | Corepressor interacting with rbpj 1 | protein | 14 | 0% helix, 0% strand | Q86X95 |
| A | Pre-mRNA-processing-splicing factor 8 | protein | 1722 | 41% helix, 8% strand | Q6P2Q9 |
| B | 116 kda U5 small nuclear ribonucleoprotein component | protein | 895 | 30% helix, 19% strand | Q15029 |
| C | Snw domain-containing protein 1 | protein | 224 | 25% helix, 5% strand | Q13573 |
| D | Pleiotropic regulator 1 | protein | 315 | 0% helix, 46% strand | O43660 |
| E | Pre-mRNA-processing factor 17 | protein | 78 | 17% helix, 6% strand | O60508 |
| F | U5 small nuclear ribonucleoprotein 40 kda protein | protein | 299 | 0% helix, 39% strand | Q96DI7 |
| L | Cell division cycle 5-like protein | protein | 202 | 50% helix, 0% strand | Q99459 |
| O | Crooked neck-like protein 1 | protein | 252 | 70% helix, 0% strand | Q9BZJ0 |
| P | Pre-mRNA-splicing factor RBM22 | protein | 195 | 26% helix, 7% strand | Q9NW64 |
| Q | Protein BUD31 homolog | protein | 142 | 41% helix, 0% strand | P41223 |
| R | Spliceosome-associated protein CWC15 homolog | protein | 87 | 26% helix, 0% strand | Q9P013 |
| S | SERINE/ARGININE repetitive matrix protein 2 | protein | 30 | 0% helix, 3% strand | Q9UQ35 |
| T | Pre-mRNA-splicing factor CWC22 homolog | protein | 203 | 65% helix, 0% strand | Q9HCG8 |
| V | Peptidyl-prolyl cis-trans isomerase-like 1 (EC 5.2.1.8) | protein | 163 | 13% helix, 28% strand | Q9Y3C6 |
| Y | Pre-mRNA | rna | 41 | — | — |
| Z | Pre-mRNA | rna | 13 | — | — |
| p | Wd repeat-containing protein 70 | protein | 325 | 0% helix, 32% strand | Q9NW82 |
| r | Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 (EC 3.6.4.13) | protein | 35 | 40% helix, 0% strand | Q92620 |
| s | Pre-mRNA-splicing factor ISY1 homolog | protein | 20 | 40% helix, 0% strand | Q9ULR0 |
| t | Pre-mRNA-splicing factor CWC25 homolog | protein | 56 | 79% helix, 0% strand | Q9NXE8 |
| u | Splicing factor YJU2 | protein | 157 | 24% helix, 23% strand | Q9BW85 |
| x | Protein FRG1 | protein | 30 | 50% helix, 0% strand | Q14331 |
Ligands and binding sites
- IHP · Inositol hexakisphosphate · ligand · chains A, x
- GTP · Guanosine-5'-triphosphate · ligand · chains A, B
- ZN · Zinc ion · metal · 7 copies · chains 6, P, Q, u
- MG · Magnesium ion · metal · 5 copies · chains 6, Y, A
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 | 1152 | 0.89 | 0.91 | 152 | IHP |
| 2 | 603 | 0.88 | 0.93 | 77 | empty |
| 3 | 932 | 0.87 | 0.89 | 82 | empty |
| 4 | 1081 | 0.85 | 0.86 | 92 | empty |
| 5 | 1016 | 0.85 | 0.86 | 116 | empty |
Interfaces
94 interfaces between chains.
- A–B · 5655 Ų buried · 58 hydrogen bonds · protein-protein
- 5–A · 3257 Ų buried · 54 hydrogen bonds · protein-nucleic
- A–C · 2498 Ų buried · 20 hydrogen bonds · protein-protein
- L–O · 2061 Ų buried · 24 hydrogen bonds · protein-protein
- A–T · 1813 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6ZYM · Human C Complex Spliceosome - High-resolution CORE · the same entry in another collection · chain L against L, 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 Q86X95
- Every structure of UniProt Q6P2Q9
- Every structure of UniProt Q15029
- Every structure of UniProt Q13573
- Every structure of UniProt O43660
- Every structure of UniProt O60508
- Every structure of UniProt Q96DI7
- Every structure of UniProt Q99459
- Every structure of UniProt Q9BZJ0
- Every structure of UniProt Q9NW64
- Every structure of UniProt P41223
- Every structure of UniProt Q9P013
- Every structure of UniProt Q9UQ35
- Every structure of UniProt Q9HCG8
- Every structure of UniProt Q9Y3C6
- Every structure of UniProt Q9NW82
- Every structure of UniProt Q92620
- Every structure of UniProt Q9ULR0
- Every structure of UniProt Q9NXE8
- Every structure of UniProt Q9BW85
- Every structure of UniProt Q14331
- Elsewhere: RCSB PDB 6ZYM · PDBe 6ZYM · UniProt Q86X95 · UniProt Q6P2Q9 · UniProt Q15029 · UniProt Q13573 · UniProt O43660 · UniProt O60508 · UniProt Q96DI7 · UniProt Q99459 · UniProt Q9BZJ0 · UniProt Q9NW64 · UniProt P41223 · UniProt Q9P013 · UniProt Q9UQ35 · UniProt Q9HCG8 · UniProt Q9Y3C6 · UniProt Q9NW82 · UniProt Q92620 · UniProt Q9ULR0 · UniProt Q9NXE8 · UniProt Q9BW85 · UniProt Q14331
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