MolNFT v1 · #135497 · protein
Cryo-EM structure of the mediator-rnapii complex
5U0S · Mediator complex subunit 6: “Cryo-EM structure of the mediator-rnapii complex”. Electron microscopy, 20 pockets (best druggability 0.86). MolNFT v1 #135497 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5U0S
- Type
- protein
- Length
- 6,861 residues
- Chains
- 28
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mediator complex subunit 6; Mediator complex subunit 8; Mediator complex subunit 17…
- EC
- 2.7.7.6
- UniProt
- Q9US45, O94646, P87306, O14198, Q10317, Q9P6Q0, O14010, Q9P7Y4, O60104, O94376, Q9USH1, Q10477, O13964, P36594, Q02061, P37382, O74825, Q09191, P36595, O14459, Q92399, O74635, O13877, P87123, P48011
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 28 distinct chains · 36% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F | Mediator complex subunit 6 | protein | 188 | 31% helix, 15% strand | Q9US45 |
| H | Mediator complex subunit 8 | protein | 182 | 74% helix, 2% strand | O94646 |
| Q | Mediator complex subunit 17 | protein | 500 | 48% helix, 8% strand | P87306 |
| R | Mediator complex subunit 18 | protein | 207 | 18% helix, 25% strand | O14198 |
| T | Mediator complex subunit 20 | protein | 176 | 16% helix, 25% strand | Q10317 |
| K | Mediator complex subunit 11 | protein | 98 | 67% helix, 0% strand | Q9P6Q0 |
| V | Mediator complex subunit 22 | protein | 118 | 69% helix, 1% strand | O14010 |
| N | Mediator complex subunit 14 | protein | 520 | 35% helix, 6% strand | Q9P7Y4 |
| D | Mediator complex subunit 4 | protein | 96 | 82% helix, 0% strand | — |
| G | Mediator complex subunit 7 | protein | 194 | 56% helix, 1% strand | O60104 |
| U | Mediator complex subunit 21 | protein | 122 | 77% helix, 0% strand | O94376 |
| 3 | Mediator complex subunit 31 | protein | 103 | 61% helix, 0% strand | Q9USH1 |
| 2 | Mediator complex subunit 27 | protein | 78 | 49% helix, 3% strand | Q10477 |
| I | Mediator complex subunit 9 | protein | 75 | 72% helix, 0% strand | O13964 |
| S | Mediator complex subunit 19 | protein | 122 | 80% helix, 0% strand | — |
| J | Mediator complex subunit 10 | protein | 131 | 85% helix, 0% strand | — |
| a | RNA polymerase II subunit RPB1 (EC 2.7.7.6) | protein | 1490 | 30% helix, 9% strand | P36594 |
| b | RNA polymerase II subunit RPB2 (EC 2.7.7.6) | protein | 1150 | 21% helix, 11% strand | Q02061 |
| c | RNA polymerase II subunit RPB3 | protein | 263 | 20% helix, 21% strand | P37382 |
| d | RNA polymerase II subunit RPB4 | protein | 125 | 58% helix, 1% strand | O74825 |
| e | RNA polymerase II subunit RPB5 | protein | 207 | 22% helix, 14% strand | Q09191 |
| f | RNA polymerase II subunit RPB6 | protein | 83 | 29% helix, 7% strand | P36595 |
| g | RNA polymerase II subunit RPB7 | protein | 170 | 11% helix, 43% strand | O14459 |
| h | RNA polymerase II subunit RPB8 | protein | 124 | 3% helix, 24% strand | Q92399 |
| i | RNA polymerase II subunit RPB9 | protein | 111 | 0% helix, 17% strand | O74635 |
| j | RNA polymerase II subunit RPB10 | protein | 64 | 31% helix, 2% strand | O13877 |
| k | RNA polymerase II subunit RPB11 | protein | 119 | 32% helix, 16% strand | P87123 |
| l | RNA polymerase II subunit RPB12 | protein | 45 | 0% helix, 13% strand | P48011 |
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 | 880 | 0.86 | 0.88 | 101 | empty |
| 2 | 713 | 0.85 | 0.89 | 75 | empty |
| 3 | 894 | 0.84 | 0.86 | 108 | empty |
| 4 | 970 | 0.81 | 0.82 | 126 | empty |
| 5 | 962 | 0.80 | 0.82 | 95 | empty |
Interfaces
74 interfaces between chains.
- a–b · 9926 Ų buried · 133 hydrogen bonds · protein-protein
- Q–V · 2401 Ų buried · 23 hydrogen bonds · protein-protein
- a–e · 2331 Ų buried · 34 hydrogen bonds · protein-protein
- a–f · 2172 Ų buried · 17 hydrogen bonds · protein-protein
- H–Q · 2015 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 1 isopeptide (disulfide, isopeptide).
Compared structures
- 5U0S · Cryo-EM structure of the Mediator-RNAPII complex · the same entry in another collection · chain R against R, 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 Q9US45
- Every structure of UniProt O94646
- Every structure of UniProt P87306
- Every structure of UniProt O14198
- Every structure of UniProt Q10317
- Every structure of UniProt Q9P6Q0
- Every structure of UniProt O14010
- Every structure of UniProt Q9P7Y4
- Every structure of UniProt O60104
- Every structure of UniProt O94376
- Every structure of UniProt Q9USH1
- Every structure of UniProt Q10477
- Every structure of UniProt O13964
- Every structure of UniProt P36594
- Every structure of UniProt Q02061
- Every structure of UniProt P37382
- Every structure of UniProt O74825
- Every structure of UniProt Q09191
- Every structure of UniProt P36595
- Every structure of UniProt O14459
- Every structure of UniProt Q92399
- Every structure of UniProt O74635
- Every structure of UniProt O13877
- Every structure of UniProt P87123
- Every structure of UniProt P48011
- Elsewhere: RCSB PDB 5U0S · PDBe 5U0S · UniProt Q9US45 · UniProt O94646 · UniProt P87306 · UniProt O14198 · UniProt Q10317 · UniProt Q9P6Q0 · UniProt O14010 · UniProt Q9P7Y4 · UniProt O60104 · UniProt O94376 · UniProt Q9USH1 · UniProt Q10477 · UniProt O13964 · UniProt P36594 · UniProt Q02061 · UniProt P37382 · UniProt O74825 · UniProt Q09191 · UniProt P36595 · UniProt O14459 · UniProt Q92399 · UniProt O74635 · UniProt O13877 · UniProt P87123 · UniProt P48011
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.