MolNFT v1 · #134138 · protein + DNA
Mediator-RNA polymerase II pre-initiation complex
5SVA · DNA-directed RNA polymerase II subunit RPB1: “Mediator-RNA polymerase II pre-initiation complex”. Electron microscopy, 2 ligands (ZN, MG), 20 pockets (best druggability 0.89). MolNFT v1 #134138 on GenesisL1: 3D structure, binding…
- PDB
- 5SVA
- Type
- protein + DNA
- Length
- 8,646 residues
- Chains
- 40
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase II subunit RPB1; DNA-directed RNA polymerase II subunit RPB2…
- EC
- 2.7.7.6, 3.6.4.12
- UniProt
- P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422, P38782, P38304, Q99278, P32569, P32585, P34162, P32570, Q12343, Q08278, P33308, P47822, P38633, P06839, Q00578, Q02939, Q3E7C1, P29055, P32773, P32774, P41895, P41896, P36100, P36145, P13393, P35189
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 40 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase II subunit RPB1 (EC 2.7.7.6) | protein | 1422 | 41% helix, 17% strand | P04050 |
| B | DNA-directed RNA polymerase II subunit RPB2 (EC 2.7.7.6) | protein | 1156 | 28% helix, 26% strand | P08518 |
| C | DNA-directed RNA polymerase II subunit RPB3 | protein | 266 | 26% helix, 29% strand | P16370 |
| D | DNA-directed RNA polymerase II subunit RPB4 | protein | 178 | 49% helix, 7% strand | P20433 |
| E | DNA-directed RNA polymerases I, II, and III subunit RPABC1 | protein | 214 | 41% helix, 24% strand | P20434 |
| F | DNA-directed RNA polymerases I, II, and III subunit RPABC2 | protein | 84 | 35% helix, 15% strand | P20435 |
| G | DNA-directed RNA polymerase II subunit RPB7 | protein | 171 | 13% helix, 50% strand | P34087 |
| H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | protein | 133 | 2% helix, 44% strand | P20436 |
| I | DNA-directed RNA polymerase II subunit RPB9 | protein | 119 | 4% helix, 30% strand | P27999 |
| J | DNA-directed RNA polymerases I, II, and III subunit RPABC5 | protein | 65 | 45% helix, 2% strand | P22139 |
| K | DNA-directed RNA polymerase II subunit RPB11 | protein | 114 | 40% helix, 24% strand | P38902 |
| L | DNA-directed RNA polymerases I, II, and III subunit RPABC4 | protein | 46 | 0% helix, 13% strand | P40422 |
| M | Mediator of RNA polymerase II transcription subunit 6 | protein | 156 | 37% helix, 22% strand | P38782 |
| N | Mediator of RNA polymerase II transcription subunit 8 | protein | 168 | 64% helix, 0% strand | P38304 |
| O | Mediator of RNA polymerase II transcription subunit 11 | protein | 103 | 85% helix, 0% strand | Q99278 |
| P | Mediator of RNA polymerase II transcription subunit 17 | protein | 487 | 46% helix, 14% strand | P32569 |
| Q | Mediator of RNA polymerase II transcription subunit 18 | protein | 253 | 24% helix, 35% strand | P32585 |
| R | Mediator of RNA polymerase II transcription subunit 20 | protein | 209 | 23% helix, 40% strand | P34162 |
| S | Mediator of RNA polymerase II transcription subunit 22 | protein | 109 | 73% helix, 0% strand | P32570 |
| T | Mediator of RNA polymerase II transcription subunit 4 | protein | 91 | 85% helix, 0% strand | Q12343 |
| U | Mediator of RNA polymerase II transcription subunit 7 | protein | 156 | 72% helix, 0% strand | Q08278 |
| V | Mediator of RNA polymerase II transcription subunit 9 | protein | 85 | 76% helix, 0% strand | P33308 |
| W | Mediator of RNA polymerase II transcription subunit 21 | protein | 119 | 78% helix, 0% strand | P47822 |
| X | Mediator of RNA polymerase II transcription subunit 31 | protein | 92 | 62% helix, 2% strand | P38633 |
| Y | DNA repair helicase RAD3 (EC 3.6.4.12) | protein | 562 | 54% helix, 14% strand | P06839 |
| Z | DNA repair helicase RAD25 (EC 3.6.4.12) | protein | 469 | 36% helix, 19% strand | Q00578 |
| a | RNA polymerase II transcription factor B subunit 2 | protein | 62 | 44% helix, 31% strand | Q02939 |
| b | RNA polymerase II transcription factor B subunit 5 | protein | 63 | 48% helix, 30% strand | Q3E7C1 |
| c | Transcription initiation factor iib | protein | 189 | 33% helix, 10% strand | P29055 |
| d | Transcription initiation factor iia large subunit | protein | 116 | 41% helix, 32% strand | P32773 |
| e | Transcription initiation factor iia subunit 2 | protein | 101 | 40% helix, 38% strand | P32774 |
| f | Transcription initiation factor iif subunit alpha | protein | 149 | 17% helix, 40% strand | P41895 |
| g | Transcription initiation factor iif subunit beta (EC 3.6.4.12) | protein | 172 | 29% helix, 31% strand | P41896 |
| h | Transcription initiation factor iie subunit alpha | protein | 118 | 45% helix, 21% strand | P36100 |
| i | Transcription initiation factor iie subunit beta | protein | 120 | 52% helix, 13% strand | P36145 |
| j | Tata-box-binding protein | protein | 180 | 27% helix, 41% strand | P13393 |
| k | DNA-directed RNA polymerase II subunit RPB1 (EC 2.7.7.6) | protein | 25 | 0% helix, 0% strand | P04050 |
| l | 108BP HIS4 promoter non-template strand (-92/+16) | dna | 62 | — | — |
| m | 108BP HIS4 promoter template strand (+16/-92) | dna | 62 | — | — |
| n | Transcription initiation factor tfiid subunit 14 | protein | 200 | 0% helix, 0% strand | P35189 |
Ligands and binding sites
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 | 1046 | 0.89 | 0.90 | 124 | empty |
| 2 | 1050 | 0.86 | 0.87 | 131 | empty |
| 3 | 1074 | 0.84 | 0.85 | 95 | empty |
| 4 | 1197 | 0.84 | 0.84 | 112 | empty |
| 5 | 1092 | 0.83 | 0.85 | 146 | empty |
Interfaces
96 interfaces between chains.
- A–B · 9806 Ų buried · 156 hydrogen bonds · protein-protein
- d–e · 2836 Ų buried · 39 hydrogen bonds · protein-protein
- A–c · 2661 Ų buried · 54 hydrogen bonds · protein-protein
- l–m · 2651 Ų buried · 153 hydrogen bonds · nucleic-nucleic
- D–G · 2454 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 isopeptide, 1 disulfide (isopeptide, disulfide).
Compared structures
- 5SVA · Mediator-RNA Polymerase II Pre-Initiation Complex · the same entry in another collection · chain F against F, 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 P04050
- Every structure of UniProt P08518
- Every structure of UniProt P16370
- Every structure of UniProt P20433
- Every structure of UniProt P20434
- Every structure of UniProt P20435
- Every structure of UniProt P34087
- Every structure of UniProt P20436
- Every structure of UniProt P27999
- Every structure of UniProt P22139
- Every structure of UniProt P38902
- Every structure of UniProt P40422
- Every structure of UniProt P38782
- Every structure of UniProt P38304
- Every structure of UniProt Q99278
- Every structure of UniProt P32569
- Every structure of UniProt P32585
- Every structure of UniProt P34162
- Every structure of UniProt P32570
- Every structure of UniProt Q12343
- Every structure of UniProt Q08278
- Every structure of UniProt P33308
- Every structure of UniProt P47822
- Every structure of UniProt P38633
- Every structure of UniProt P06839
- Every structure of UniProt Q00578
- Every structure of UniProt Q02939
- Every structure of UniProt Q3E7C1
- Every structure of UniProt P29055
- Every structure of UniProt P32773
- Every structure of UniProt P32774
- Every structure of UniProt P41895
- Every structure of UniProt P41896
- Every structure of UniProt P36100
- Every structure of UniProt P36145
- Every structure of UniProt P13393
- Every structure of UniProt P35189
- Elsewhere: RCSB PDB 5SVA · PDBe 5SVA · UniProt P04050 · UniProt P08518 · UniProt P16370 · UniProt P20433 · UniProt P20434 · UniProt P20435 · UniProt P34087 · UniProt P20436 · UniProt P27999 · UniProt P22139 · UniProt P38902 · UniProt P40422 · UniProt P38782 · UniProt P38304 · UniProt Q99278 · UniProt P32569 · UniProt P32585 · UniProt P34162 · UniProt P32570 · UniProt Q12343 · UniProt Q08278 · UniProt P33308 · UniProt P47822 · UniProt P38633 · UniProt P06839 · UniProt Q00578 · UniProt Q02939 · UniProt Q3E7C1 · UniProt P29055 · UniProt P32773 · UniProt P32774 · UniProt P41895 · UniProt P41896 · UniProt P36100 · UniProt P36145 · UniProt P13393 · UniProt P35189
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