MolNFT v1 · #122735 · protein + DNA
Human holo-pic in the initial transcribing state
5IY8 · DNA-directed RNA polymerase II subunit RPB1: “Human holo-pic in the initial transcribing state”. Electron microscopy, 2 ligands (ZN, MG), 20 pockets (best druggability 0.89). MolNFT v1 #122735 on GenesisL1: 3D structure, binding…
- PDB
- 5IY8
- Type
- protein + DNA
- Length
- 7,600 residues
- Chains
- 29
- 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, P23193, P19447, P18074, Q13888, Q6ZYL4, Q92759, Q13889
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 29 distinct chains · 38% helix, 19% 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 | 30% helix, 24% strand | P30876 |
| C | DNA-directed RNA polymerase II subunit RPB3 | protein | 275 | 21% helix, 26% strand | P19387 |
| D | DNA-directed RNA polymerase II subunit RPB4 | protein | 129 | 64% helix, 3% strand | O15514 |
| E | DNA-directed RNA polymerase II subunit RPB5 | protein | 210 | 43% helix, 22% strand | P19388 |
| F | DNA-directed RNA polymerase II subunit RPB6 | protein | 86 | 35% helix, 15% strand | P61218 |
| G | DNA-directed RNA polymerase II subunit RPB7 | protein | 171 | 11% helix, 53% strand | P62487 |
| H | DNA-directed RNA polymerase II subunit RPB8 | protein | 150 | 2% helix, 41% 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, 23% strand | P52435 |
| L | DNA-directed RNA polymerase II subunit RPB12 | protein | 46 | 0% helix, 9% strand | P53803 |
| M | Transcription initiation factor iib | protein | 310 | 44% helix, 3% strand | Q00403 |
| N | Transcription initiation factor iia subunit 1 | protein | 113 | 41% helix, 33% strand | P52655 |
| O | Transcription initiation factor iia subunit 2 | protein | 99 | 41% helix, 38% strand | P52657 |
| P | Tata-box-binding protein | protein | 185 | 29% helix, 32% strand | P20226 |
| Q | General transcription factor iie subunit 1 | protein | 180 | 56% helix, 10% strand | P29083 |
| R | Transcription initiation factor iie subunit beta | protein | 165 | 43% helix, 10% strand | P29084 |
| S | General transcription factor iif subunit 1 | protein | 138 | 16% helix, 37% strand | P35269 |
| T | General transcription factor iif subunit 2 (EC 3.6.4.12) | protein | 222 | 32% helix, 30% strand | P13984 |
| U | Transcription elongation factor a protein 1 | protein | 170 | 48% helix, 6% strand | P23193 |
| V | Tfiih basal transcription factor complex helicase xpb subunit (EC 3.6.4.12) | protein | 475 | 36% helix, 17% strand | P19447 |
| W | Tfiih basal transcription factor complex helicase xpd subunit (EC 3.6.4.12) | protein | 665 | 49% helix, 11% strand | P18074 |
| 0 | General transcription factor iih subunit 2 | protein | 188 | 43% helix, 25% strand | Q13888 |
| 1 | General transcription factor iih subunit 5 | protein | 62 | 31% helix, 26% strand | Q6ZYL4 |
| 2 | General transcription factor iih subunit 4 | protein | 274 | 66% helix, 5% strand | Q92759 |
| 3 | General transcription factor iih subunit 3 | protein | 193 | 52% helix, 21% strand | Q13889 |
| X | Scp-X | dna | 83 | — | — |
| Y | Scp-Y | dna | 83 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 11 copies · chains A, B, C, I, J, L, M, Q, U
- MG · Magnesium ion · metal · 2 copies · chains A, U, 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 | 1085 | 0.89 | 0.90 | 125 | empty |
| 2 | 605 | 0.88 | 0.94 | 71 | empty |
| 3 | 997 | 0.87 | 0.88 | 102 | empty |
| 4 | 1049 | 0.87 | 0.88 | 110 | empty |
| 5 | 870 | 0.85 | 0.88 | 88 | empty |
Interfaces
77 interfaces between chains.
- A–B · 9353 Ų buried · 90 hydrogen bonds · protein-protein
- A–U · 3316 Ų buried · 36 hydrogen bonds · protein-protein
- X–Y · 2991 Ų buried · 326 hydrogen bonds · nucleic-nucleic
- N–O · 2804 Ų buried · 32 hydrogen bonds · protein-protein
- A–M · 2510 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 5IY8 · Human holo-PIC in the initial transcribing state · the same entry in another collection · chain J against J, 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
- Every structure of UniProt P23193
- Every structure of UniProt P19447
- Every structure of UniProt P18074
- Every structure of UniProt Q13888
- Every structure of UniProt Q6ZYL4
- Every structure of UniProt Q92759
- Every structure of UniProt Q13889
- Elsewhere: RCSB PDB 5IY8 · PDBe 5IY8 · 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 · UniProt P23193 · UniProt P19447 · UniProt P18074 · UniProt Q13888 · UniProt Q6ZYL4 · UniProt Q92759 · UniProt Q13889
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