MolNFT v1 · #122740 · protein + DNA + RNA
Human core-pic in the initial transcribing state (no iis)
5IYD · DNA-directed RNA polymerase II subunit RPB1: “Human core-pic in the initial transcribing state (no iis)”. Electron microscopy, 2 ligands (ZN, MG), 20 pockets (best druggability 0.89). MolNFT v1 #122740 on GenesisL1: 3D structure…
- PDB
- 5IYD
- Type
- protein + DNA + RNA
- Length
- 5,573 residues
- Chains
- 23
- 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, 2.7.7.48, 3.6.4.12
- UniProt
- P24928, P30876, P19387, O15514, P19388, P61218, P62487, P52434, P36954, P62875, P52435, P53803, Q00403, P52655, P52657, P20226, P29083, P29084, P35269, P13984
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 23 distinct chains · 35% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase II subunit RPB1 (EC 2.7.7.6, 2.7.7.48) | protein | 1454 | 42% helix, 13% strand | P24928 |
| B | DNA-directed RNA polymerase II subunit RPB2 (EC 2.7.7.6) | protein | 1165 | 31% helix, 24% strand | P30876 |
| C | DNA-directed RNA polymerase II subunit RPB3 | protein | 275 | 24% helix, 27% strand | P19387 |
| D | DNA-directed RNA polymerase II subunit RPB4 | protein | 129 | 66% helix, 3% strand | O15514 |
| E | DNA-directed RNA polymerase II subunit RPB5 | protein | 210 | 42% helix, 21% strand | P19388 |
| F | DNA-directed RNA polymerase II subunit RPB6 | protein | 86 | 30% helix, 17% strand | P61218 |
| G | DNA-directed RNA polymerase II subunit RPB7 | protein | 171 | 9% helix, 54% strand | P62487 |
| H | DNA-directed RNA polymerase II subunit RPB8 | protein | 150 | 0% helix, 43% strand | P52434 |
| I | DNA-directed RNA polymerase II subunit RPB9 | protein | 125 | 4% helix, 28% strand | P36954 |
| J | DNA-directed RNA polymerase II subunit RPB10 | protein | 67 | 49% helix, 1% strand | P62875 |
| K | DNA-directed RNA polymerase II subunit RPB11-a | protein | 117 | 38% helix, 25% strand | P52435 |
| L | DNA-directed RNA polymerase II subunit RPB12 | protein | 46 | 0% helix, 9% strand | P53803 |
| M | Transcription initiation factor iib | protein | 310 | 47% helix, 3% strand | Q00403 |
| N | Transcription initiation factor iia subunit 1 | protein | 113 | 37% helix, 35% strand | P52655 |
| O | Transcription initiation factor iia subunit 2 | protein | 99 | 41% helix, 40% strand | P52657 |
| P | Tata-box-binding protein | protein | 185 | 29% helix, 31% strand | P20226 |
| Q | General transcription factor iie subunit 1 | protein | 180 | 53% helix, 9% strand | P29083 |
| R | Transcription initiation factor iie subunit beta | protein | 165 | 44% helix, 10% strand | P29084 |
| S | General transcription factor iif subunit 1 | protein | 138 | 13% helix, 39% strand | P35269 |
| T | General transcription factor iif subunit 2 (EC 3.6.4.12) | protein | 222 | 31% helix, 30% strand | P13984 |
| X | Scp-X | dna | 80 | — | — |
| Y | Scp-Y | dna | 80 | — | — |
| Z | RNA | rna | 6 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 11 copies · chains A, B, I, J, L, M, Q
- MG · Magnesium ion · metal · 2 copies · chains A, Z, 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 | 1136 | 0.89 | 0.90 | 124 | empty |
| 2 | 990 | 0.88 | 0.90 | 102 | empty |
| 3 | 890 | 0.87 | 0.89 | 94 | empty |
| 4 | 753 | 0.86 | 0.89 | 89 | empty |
| 5 | 601 | 0.85 | 0.91 | 70 | empty |
Interfaces
66 interfaces between chains.
- A–B · 9232 Ų buried · 120 hydrogen bonds · protein-protein
- X–Y · 2794 Ų buried · 373 hydrogen bonds · nucleic-nucleic
- N–O · 2727 Ų buried · 28 hydrogen bonds · protein-protein
- A–M · 2530 Ų buried · 27 hydrogen bonds · protein-protein
- C–K · 2416 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 5IYD · Human core-PIC in the initial transcribing state (no IIS) · 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 P24928
- Every structure of UniProt P30876
- Every structure of UniProt P19387
- Every structure of UniProt O15514
- Every structure of UniProt P19388
- Every structure of UniProt P61218
- Every structure of UniProt P62487
- Every structure of UniProt P52434
- Every structure of UniProt P36954
- Every structure of UniProt P62875
- Every structure of UniProt P52435
- Every structure of UniProt P53803
- Every structure of UniProt Q00403
- Every structure of UniProt P52655
- Every structure of UniProt P52657
- Every structure of UniProt P20226
- Every structure of UniProt P29083
- Every structure of UniProt P29084
- Every structure of UniProt P35269
- Every structure of UniProt P13984
- Elsewhere: RCSB PDB 5IYD · PDBe 5IYD · UniProt P24928 · UniProt P30876 · UniProt P19387 · UniProt O15514 · UniProt P19388 · UniProt P61218 · UniProt P62487 · UniProt P52434 · UniProt P36954 · UniProt P62875 · UniProt P52435 · UniProt P53803 · UniProt Q00403 · UniProt P52655 · UniProt P52657 · UniProt P20226 · UniProt P29083 · UniProt P29084 · UniProt P35269 · UniProt P13984
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