MolNFT v1 · #148124 · protein + RNA
Post-catalytic P complex spliceosome with 3' splice site docked
6EXN · U2 snrna: “Post-catalytic P complex spliceosome with 3' splice site docked”. Electron microscopy, 4 ligands (IHP, GTP, ZN), 20 pockets (best druggability 0.89). MolNFT v1 #148124 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6EXN
- Type
- protein + RNA
- Length
- 9,948 residues
- Chains
- 46
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- U2 snrna; U5 snrna; U6 snrna; Pre-mRNA-splicing factor PRP8; Pre-mRNA-splicing factor…
- EC
- 3.6.4.13, 2.3.2.27
- UniProt
- P33334, P36048, P28320, P53333, Q12417, P28004, P25337, Q12046, P38241, Q03654, Q03772, Q03375, Q12309, Q04048, P24384, Q08963, P40567, P33411, P40018, Q02775, P43321, Q12330, P54999, P40204, Q02260, Q06217, P40968, Q06091, P32523, P53277
- Ligands
- IHP, GTP, ZN, MG
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 45 distinct chains · 44% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 2 | U2 snrna | rna | 136 | — | — |
| 5 | U5 snrna | rna | 171 | — | — |
| 6 | U6 snrna | rna | 102 | — | — |
| A | Pre-mRNA-splicing factor PRP8 | protein | 1945 | 43% helix, 10% strand | P33334 |
| C | Pre-mRNA-splicing factor SNU114 | protein | 880 | 36% helix, 20% strand | P36048 |
| D | Pre-mRNA-splicing factor CWC16 | protein | 97 | 86% helix, 0% strand | P28320 |
| E | Ligated exons: UBC4 mRNA | rna | 32 | — | — |
| H | Pre-mRNA-splicing factor CWC22 | protein | 411 | 73% helix, 0% strand | P53333 |
| I | Intron lariat: UBC4 RNA | rna | 38 | — | — |
| J | Pre-mRNA-splicing factor PRP46 | protein | 342 | 4% helix, 43% strand | Q12417 |
| K | Pre-mRNA-processing protein 45 | protein | 170 | 34% helix, 4% strand | P28004 |
| L | Pre-mRNA-splicing factor BUD31 | protein | 156 | 49% helix, 0% strand | P25337 |
| M | Pre-mRNA-splicing factor CWC2 | protein | 255 | 28% helix, 13% strand | Q12046 |
| N | Pre-mRNA-splicing factor SLT11 | protein | 242 | 36% helix, 20% strand | P38241 |
| O | Pre-mRNA-splicing factor CEF1 | protein | 320 | 64% helix, 1% strand | Q03654 |
| P | Pre-mRNA-splicing factor CWC15 | protein | 73 | 21% helix, 0% strand | Q03772 |
| R | Pre-mRNA-splicing factor CWC21 | protein | 73 | 59% helix, 3% strand | Q03375 |
| S | Pre-mRNA-splicing factor CLF1 | protein | 472 | 82% helix, 0% strand | Q12309 |
| T | Pre-mRNA-splicing factor SYF1 | protein | 594 | 84% helix, 0% strand | Q04048 |
| V | Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP22 (EC 3.6.4.13) | protein | 638 | 42% helix, 18% strand | P24384 |
| W | U2 small nuclear ribonucleoprotein a' | protein | 149 | 11% helix, 13% strand | Q08963 |
| X | Unassigned structure | protein | 95 | 87% helix, 0% strand | — |
| Y | U2 small nuclear ribonucleoprotein B'' | protein | 87 | 24% helix, 28% strand | P40567 |
| a | Pre-mRNA-splicing factor PRP18 | protein | 171 | 61% helix, 1% strand | P33411 |
| b | Small nuclear ribonucleoprotein-associated protein B | protein | 80 | 4% helix, 48% strand | P40018 |
| c | Pre-mRNA-splicing factor SLU7 | protein | 204 | 29% helix, 3% strand | Q02775 |
| d, n | Small nuclear ribonucleoprotein sm D3 | protein | 82 | 17% helix, 39% strand | P43321 |
| e | Small nuclear ribonucleoprotein E | protein | 75 | 15% helix, 32% strand | Q12330 |
| f | Small nuclear ribonucleoprotein F | protein | 72 | 6% helix, 40% strand | P54999 |
| g | Small nuclear ribonucleoprotein G | protein | 69 | 0% helix, 41% strand | P40204 |
| h | Small nuclear ribonucleoprotein sm D1 | protein | 82 | 9% helix, 34% strand | Q02260 |
| j | Small nuclear ribonucleoprotein sm D2 | protein | 94 | 14% helix, 37% strand | Q06217 |
| k | Small nuclear ribonucleoprotein-associated protein B | protein | 70 | 0% helix, 57% strand | P40018 |
| l | Small nuclear ribonucleoprotein sm D1 | protein | 87 | 15% helix, 44% strand | Q02260 |
| m | Small nuclear ribonucleoprotein sm D2 | protein | 92 | 24% helix, 48% strand | Q06217 |
| o | Pre-mRNA-processing factor PRP17 | protein | 322 | 2% helix, 31% strand | P40968 |
| p | Small nuclear ribonucleoprotein E | protein | 77 | 17% helix, 43% strand | Q12330 |
| q | Small nuclear ribonucleoprotein F | protein | 73 | 12% helix, 58% strand | P54999 |
| r | Small nuclear ribonucleoprotein G | protein | 75 | 8% helix, 49% strand | P40204 |
| s | Pre-mRNA-splicing factor SNT309 | protein | 110 | 69% helix, 0% strand | Q06091 |
| t | Pre-mRNA-processing factor PRP19 (EC 2.3.2.27) | protein | 117 | 63% helix, 5% strand | P32523 |
| u | Pre-mRNA-processing factor PRP19 (EC 2.3.2.27) | protein | 116 | 60% helix, 8% strand | P32523 |
| v | Pre-mRNA-processing factor PRP19 (EC 2.3.2.27) | protein | 118 | 63% helix, 5% strand | P32523 |
| w | Pre-mRNA-processing factor PRP19 (EC 2.3.2.27) | protein | 114 | 60% helix, 5% strand | P32523 |
| y | Pre-mRNA-splicing factor SYF2 | protein | 88 | 67% helix, 7% strand | P53277 |
Ligands and binding sites
- IHP · Inositol hexakisphosphate · ligand · chains A, c
- GTP · Guanosine-5'-triphosphate · ligand · chains A, C
- ZN · Zinc ion · metal · 7 copies · chains L, 6, M, N, c
- MG · Magnesium ion · metal · chains 6, E, I
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 | 1040 | 0.89 | 0.91 | 113 | empty |
| 2 | 1134 | 0.89 | 0.91 | 99 | GTP |
| 3 | 882 | 0.89 | 0.92 | 101 | empty |
| 4 | 772 | 0.87 | 0.91 | 88 | empty |
| 5 | 1197 | 0.87 | 0.88 | 103 | empty |
Interfaces
157 interfaces between chains.
- A–c · 7340 Ų buried · 76 hydrogen bonds · protein-protein
- A–C · 5205 Ų buried · 63 hydrogen bonds · protein-protein
- 5–A · 4064 Ų buried · 94 hydrogen bonds · protein-nucleic
- O–S · 2702 Ų buried · 27 hydrogen bonds · protein-protein
- A–K · 2444 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 6EXN · Post-catalytic P complex spliceosome with 3' splice site docked · the same entry in another collection · chain I against I, 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 P33334
- Every structure of UniProt P36048
- Every structure of UniProt P28320
- Every structure of UniProt P53333
- Every structure of UniProt Q12417
- Every structure of UniProt P28004
- Every structure of UniProt P25337
- Every structure of UniProt Q12046
- Every structure of UniProt P38241
- Every structure of UniProt Q03654
- Every structure of UniProt Q03772
- Every structure of UniProt Q03375
- Every structure of UniProt Q12309
- Every structure of UniProt Q04048
- Every structure of UniProt P24384
- Every structure of UniProt Q08963
- Every structure of UniProt P40567
- Every structure of UniProt P33411
- Every structure of UniProt P40018
- Every structure of UniProt Q02775
- Every structure of UniProt P43321
- Every structure of UniProt Q12330
- Every structure of UniProt P54999
- Every structure of UniProt P40204
- Every structure of UniProt Q02260
- Every structure of UniProt Q06217
- Every structure of UniProt P40968
- Every structure of UniProt Q06091
- Every structure of UniProt P32523
- Every structure of UniProt P53277
- Elsewhere: RCSB PDB 6EXN · PDBe 6EXN · UniProt P33334 · UniProt P36048 · UniProt P28320 · UniProt P53333 · UniProt Q12417 · UniProt P28004 · UniProt P25337 · UniProt Q12046 · UniProt P38241 · UniProt Q03654 · UniProt Q03772 · UniProt Q03375 · UniProt Q12309 · UniProt Q04048 · UniProt P24384 · UniProt Q08963 · UniProt P40567 · UniProt P33411 · UniProt P40018 · UniProt Q02775 · UniProt P43321 · UniProt Q12330 · UniProt P54999 · UniProt P40204 · UniProt Q02260 · UniProt Q06217 · UniProt P40968 · UniProt Q06091 · UniProt P32523 · UniProt P53277
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