Research workbench
Human mediator (deletion of MED1-idr) in a tail-bent conformation (med-B)
Analyse Human mediator (deletion of MED1-idr) in a tail-bent conformation (med-B) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ENJ
- Type
- protein
- Length
- 7,360 residues
- Chains
- 26
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mediator of RNA polymerase II transcription subunit 1; Unknown chain; Mediator of RNA…
- UniProt
- Q15648, Q9NPJ6, O75586, O43513, Q96G25, Q9NWA0, Q9BTT4, Q9P086, O60244, Q96RN5, Q9Y2X0, Q9NVC6, Q9BUE0, A0JLT2, Q9H944, Q13503, Q15528, Q9ULK4, O75448, O95402, Q6P2C8, Q9H204, Q9NX70, Q96HR3, Q9Y3C7
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 26 distinct chains · 52% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mediator of RNA polymerase II transcription subunit 1 | protein | 467 | 39% helix, 22% strand | Q15648 |
| B | Unknown chain | protein | 20 | 60% helix, 0% strand | — |
| D | Mediator of RNA polymerase II transcription subunit 4 | protein | 158 | 78% helix, 1% strand | Q9NPJ6 |
| F | Mediator of RNA polymerase II transcription subunit 6 | protein | 167 | 36% helix, 26% strand | O75586 |
| G | Mediator of RNA polymerase II transcription subunit 7 | protein | 161 | 63% helix, 0% strand | O43513 |
| H | Isoform 2 of mediator of RNA polymerase II transcription subunit 8 | protein | 181 | 65% helix, 2% strand | Q96G25 |
| I | Mediator of RNA polymerase II transcription subunit 9 | protein | 73 | 75% helix, 0% strand | Q9NWA0 |
| J | Mediator of RNA polymerase II transcription subunit 10 | protein | 122 | 84% helix, 0% strand | Q9BTT4 |
| K | Mediator of RNA polymerase II transcription subunit 11 | protein | 112 | 81% helix, 0% strand | Q9P086 |
| N | Mediator of RNA polymerase II transcription subunit 14 | protein | 1017 | 39% helix, 20% strand | O60244 |
| O | Mediator of RNA polymerase II transcription subunit 15 | protein | 157 | 43% helix, 8% strand | Q96RN5 |
| P | Mediator of RNA polymerase II transcription subunit 16 | protein | 420 | 6% helix, 46% strand | Q9Y2X0 |
| Q | Mediator of RNA polymerase II transcription subunit 17 | protein | 551 | 37% helix, 19% strand | Q9NVC6 |
| R | Mediator of RNA polymerase II transcription subunit 18 | protein | 191 | 16% helix, 44% strand | Q9BUE0 |
| S | Mediator of RNA polymerase II transcription subunit 19 | protein | 75 | 44% helix, 0% strand | A0JLT2 |
| T | Mediator of RNA polymerase II transcription subunit 20 | protein | 193 | 29% helix, 37% strand | Q9H944 |
| U | Mediator of RNA polymerase II transcription subunit 21 | protein | 121 | 84% helix, 0% strand | Q13503 |
| V | Mediator of RNA polymerase II transcription subunit 22 | protein | 130 | 88% helix, 0% strand | Q15528 |
| W | Mediator of RNA polymerase II transcription subunit 23 | protein | 1334 | 61% helix, 1% strand | Q9ULK4 |
| X | Mediator of RNA polymerase II transcription subunit 24 | protein | 897 | 71% helix, 0% strand | O75448 |
| Z | Mediator of RNA polymerase II transcription subunit 26 | protein | 97 | 23% helix, 10% strand | O95402 |
| 0 | Mediator of RNA polymerase II transcription subunit 27 | protein | 267 | 51% helix, 12% strand | Q6P2C8 |
| 1 | Mediator of RNA polymerase II transcription subunit 28 | protein | 99 | 85% helix, 0% strand | Q9H204 |
| 2 | Mediator of RNA polymerase II transcription subunit 29 | protein | 115 | 84% helix, 0% strand | Q9NX70 |
| 3 | Mediator of RNA polymerase II transcription subunit 30 | protein | 122 | 81% helix, 1% strand | Q96HR3 |
| 4 | Mediator of RNA polymerase II transcription subunit 31 | protein | 113 | 77% helix, 0% strand | Q9Y3C7 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains 0
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 | 973 | 0.86 | 0.88 | 86 | empty |
| 2 | 1173 | 0.86 | 0.87 | 114 | empty |
| 3 | 615 | 0.83 | 0.88 | 57 | empty |
| 4 | 1164 | 0.82 | 0.83 | 137 | empty |
| 5 | 612 | 0.81 | 0.86 | 74 | empty |
Interfaces
80 interfaces between chains.
- N–Q · 4079 Ų buried · 30 hydrogen bonds · protein-protein
- P–X · 2299 Ų buried · 15 hydrogen bonds · protein-protein
- H–Q · 2242 Ų buried · 17 hydrogen bonds · protein-protein
- 1–3 · 2058 Ų buried · 18 hydrogen bonds · protein-protein
- U–Z · 1999 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 7ENJ · Human Mediator (deletion of MED1-IDR) in a Tail-bent conformation (MED-B) · the same entry in another collection · chain K against K, 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 Q15648
- Every structure of UniProt Q9NPJ6
- Every structure of UniProt O75586
- Every structure of UniProt O43513
- Every structure of UniProt Q96G25
- Every structure of UniProt Q9NWA0
- Every structure of UniProt Q9BTT4
- Every structure of UniProt Q9P086
- Every structure of UniProt O60244
- Every structure of UniProt Q96RN5
- Every structure of UniProt Q9Y2X0
- Every structure of UniProt Q9NVC6
- Every structure of UniProt Q9BUE0
- Every structure of UniProt A0JLT2
- Every structure of UniProt Q9H944
- Every structure of UniProt Q13503
- Every structure of UniProt Q15528
- Every structure of UniProt Q9ULK4
- Every structure of UniProt O75448
- Every structure of UniProt O95402
- Every structure of UniProt Q6P2C8
- Every structure of UniProt Q9H204
- Every structure of UniProt Q9NX70
- Every structure of UniProt Q96HR3
- Every structure of UniProt Q9Y3C7
- Elsewhere: RCSB PDB 7ENJ · PDBe 7ENJ · UniProt Q15648 · UniProt Q9NPJ6 · UniProt O75586 · UniProt O43513 · UniProt Q96G25 · UniProt Q9NWA0 · UniProt Q9BTT4 · UniProt Q9P086 · UniProt O60244 · UniProt Q96RN5 · UniProt Q9Y2X0 · UniProt Q9NVC6 · UniProt Q9BUE0 · UniProt A0JLT2 · UniProt Q9H944 · UniProt Q13503 · UniProt Q15528 · UniProt Q9ULK4 · UniProt O75448 · UniProt O95402 · UniProt Q6P2C8 · UniProt Q9H204 · UniProt Q9NX70 · UniProt Q96HR3 · UniProt Q9Y3C7
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