Research workbench
S. cerevisiae spliceosomal post-catalytic P complex
Analyse S. cerevisiae spliceosomal post-catalytic P complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BK8
- Type
- protein + RNA
- Length
- 10,643 residues
- Chains
- 46
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- U2 snrna; U5 snrna; U6 snrna; RNA (34-mer); RNA (59-mer); Pre-mRNA-splicing factor PRP8…
- EC
- 3.6.4.13, 2.3.2.27
- UniProt
- P33334, P36048, Q12417, P28004, P38241, Q12046, Q03772, P25337, Q03375, P53333, P40968, P33411, Q02775, P24384, P53277, Q03654, Q12309, Q04048, Q06217, P54999, Q12330, P40204, P40018, P43321, Q02260, P40567, Q08963, P32523, Q06091
- Ligands
- IHP, GTP, ZN, MG
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 43 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 2 | U2 snrna | rna | 135 | — | — |
| 5 | U5 snrna | rna | 103 | — | — |
| 6 | U6 snrna | rna | 102 | — | — |
| e | RNA (34-mer) | rna | 34 | — | — |
| i | RNA (59-mer) | rna | 59 | — | — |
| A | Pre-mRNA-splicing factor PRP8 | protein | 1960 | 45% helix, 11% strand | P33334 |
| B | Pre-mRNA-splicing factor SNU114 | protein | 899 | 35% helix, 21% strand | P36048 |
| D | Pre-mRNA-splicing factor PRP46 | protein | 359 | 5% helix, 41% strand | Q12417 |
| E | Pre-mRNA-processing protein 45 | protein | 186 | 36% helix, 4% strand | P28004 |
| F | Pre-mRNA-splicing factor SLT11 | protein | 199 | 35% helix, 13% strand | P38241 |
| G | Pre-mRNA-splicing factor CWC2 | protein | 255 | 27% helix, 13% strand | Q12046 |
| H | Pre-mRNA-splicing factor CWC15 | protein | 70 | 17% helix, 1% strand | Q03772 |
| I | Pre-mRNA-splicing factor BUD31 | protein | 156 | 48% helix, 0% strand | P25337 |
| K | Pre-mRNA-splicing factor CWC21 | protein | 82 | 66% helix, 4% strand | Q03375 |
| L | Pre-mRNA-splicing factor CWC22 | protein | 412 | 71% helix, 0% strand | P53333 |
| M | Pre-mRNA-processing factor PRP17 | protein | 326 | 3% helix, 43% strand | P40968 |
| N | Pre-mRNA-splicing factor PRP18 | protein | 167 | 65% helix, 0% strand | P33411 |
| O | Pre-mRNA-splicing factor SLU7 | protein | 229 | 32% helix, 7% strand | Q02775 |
| P | Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP22 (EC 3.6.4.13) | protein | 653 | 42% helix, 17% strand | P24384 |
| R | Pre-mRNA-splicing factor SYF2 | protein | 101 | 64% helix, 8% strand | P53277 |
| S | Pre-mRNA-splicing factor CEF1 | protein | 238 | 55% helix, 2% strand | Q03654 |
| T | Pre-mRNA-splicing factor CLF1 | protein | 483 | 81% helix, 0% strand | Q12309 |
| U | Pre-mRNA-splicing factor SYF1 | protein | 637 | 77% helix, 0% strand | Q04048 |
| X | Unknown protein fragment | protein | 219 | 73% helix, 1% strand | — |
| Y | Unknown protein fragment | protein | 16 | 88% helix, 0% strand | — |
| a | Small nuclear ribonucleoprotein sm D2 | protein | 94 | 23% helix, 43% strand | Q06217 |
| b, m | Small nuclear ribonucleoprotein F | protein | 72 | 10% helix, 47% strand | P54999 |
| c, l | Small nuclear ribonucleoprotein E | protein | 75 | 19% helix, 32% strand | Q12330 |
| d, n | Small nuclear ribonucleoprotein G | protein | 69 | 0% helix, 45% strand | P40204 |
| f | Small nuclear ribonucleoprotein-associated protein B | protein | 80 | 4% helix, 49% strand | P40018 |
| g | Small nuclear ribonucleoprotein sm D3 | protein | 82 | 13% helix, 38% strand | P43321 |
| h | Small nuclear ribonucleoprotein sm D1 | protein | 82 | 15% helix, 44% strand | Q02260 |
| k | Small nuclear ribonucleoprotein-associated protein B | protein | 78 | 0% helix, 32% strand | P40018 |
| o | Small nuclear ribonucleoprotein sm D3 | protein | 78 | 10% helix, 41% strand | P43321 |
| p | Small nuclear ribonucleoprotein sm D1 | protein | 79 | 8% helix, 14% strand | Q02260 |
| q | Small nuclear ribonucleoprotein sm D2 | protein | 93 | 17% helix, 34% strand | Q06217 |
| r | LEA1 | protein | 84 | 26% helix, 18% strand | P40567 |
| s | MSL1 | protein | 164 | 21% helix, 5% strand | Q08963 |
| u | Pre-mRNA-processing factor PRP19 (EC 2.3.2.27) | protein | 435 | 16% helix, 40% 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 | 438 | 17% helix, 39% strand | P32523 |
| x | Pre-mRNA-processing factor PRP19 (EC 2.3.2.27) | protein | 116 | 60% helix, 8% strand | P32523 |
| y | Pre-mRNA-splicing factor SNT309 | protein | 110 | 69% helix, 0% strand | Q06091 |
Ligands and binding sites
- IHP · Inositol hexakisphosphate · ligand · chains A, O
- GTP · Guanosine-5'-triphosphate · ligand · chains B
- ZN · Zinc ion · metal · 7 copies · chains F, G, I, O
- MG · Magnesium ion · metal · 5 copies · chains 6, e, B
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 | 933 | 0.89 | 0.92 | 111 | MG |
| 2 | 1056 | 0.89 | 0.91 | 122 | empty |
| 3 | 1050 | 0.88 | 0.90 | 106 | empty |
| 4 | 905 | 0.88 | 0.91 | 86 | empty |
| 5 | 788 | 0.86 | 0.90 | 84 | MG |
Interfaces
148 interfaces between chains.
- A–O · 7341 Ų buried · 64 hydrogen bonds · protein-protein
- A–B · 5182 Ų buried · 44 hydrogen bonds · protein-protein
- 5–A · 3653 Ų buried · 61 hydrogen bonds · protein-nucleic
- S–T · 2509 Ų buried · 30 hydrogen bonds · protein-protein
- e–A · 2277 Ų buried · 17 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6BK8 · S. cerevisiae spliceosomal post-catalytic P complex · the same entry in another collection · chain G against G, 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 Q12417
- Every structure of UniProt P28004
- Every structure of UniProt P38241
- Every structure of UniProt Q12046
- Every structure of UniProt Q03772
- Every structure of UniProt P25337
- Every structure of UniProt Q03375
- Every structure of UniProt P53333
- Every structure of UniProt P40968
- Every structure of UniProt P33411
- Every structure of UniProt Q02775
- Every structure of UniProt P24384
- Every structure of UniProt P53277
- Every structure of UniProt Q03654
- Every structure of UniProt Q12309
- Every structure of UniProt Q04048
- Every structure of UniProt Q06217
- Every structure of UniProt P54999
- Every structure of UniProt Q12330
- Every structure of UniProt P40204
- Every structure of UniProt P40018
- Every structure of UniProt P43321
- Every structure of UniProt Q02260
- Every structure of UniProt P40567
- Every structure of UniProt Q08963
- Every structure of UniProt P32523
- Every structure of UniProt Q06091
- Elsewhere: RCSB PDB 6BK8 · PDBe 6BK8 · UniProt P33334 · UniProt P36048 · UniProt Q12417 · UniProt P28004 · UniProt P38241 · UniProt Q12046 · UniProt Q03772 · UniProt P25337 · UniProt Q03375 · UniProt P53333 · UniProt P40968 · UniProt P33411 · UniProt Q02775 · UniProt P24384 · UniProt P53277 · UniProt Q03654 · UniProt Q12309 · UniProt Q04048 · UniProt Q06217 · UniProt P54999 · UniProt Q12330 · UniProt P40204 · UniProt P40018 · UniProt P43321 · UniProt Q02260 · UniProt P40567 · UniProt Q08963 · UniProt P32523 · UniProt Q06091
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