MolNFT v1 · #86608 · protein + DNA + RNA
Structure of an initially transcribing RNA polymerase II- tfiib complex
4BBS · DNA-directed RNA polymerase II subunit RPB1: “Structure of an initially transcribing RNA polymerase II- tfiib complex”. X-ray diffraction, 2 ligands (ZN, MG), 20 pockets (best druggability 0.88). MolNFT v1 #86608 on GenesisL1: 3D…
- PDB
- 4BBS
- Type
- protein + DNA + RNA
- Length
- 4,180 residues
- Chains
- 16
- Method
- x-ray diffraction
- 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
- UniProt
- P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422, P29055
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 16 distinct chains · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase II subunit RPB1 (EC 2.7.7.6) | protein | 1419 | 42% helix, 16% strand | P04050 |
| B | DNA-directed RNA polymerase II subunit RPB2 (EC 2.7.7.6) | protein | 1150 | 27% helix, 25% strand | P08518 |
| C | DNA-directed RNA polymerase II subunit RPB3 | protein | 266 | 26% helix, 27% strand | P16370 |
| D | DNA-directed RNA polymerase II subunit RPB4 | protein | 178 | 51% helix, 4% strand | P20433 |
| E | DNA-directed RNA polymerases I, II, and III subunit rpabc 1 | protein | 214 | 39% helix, 22% strand | P20434 |
| F | DNA-directed RNA polymerases I, II, and III subunit rpabc 2 | protein | 87 | 29% helix, 16% strand | P20435 |
| G | DNA-directed RNA polymerase II subunit RPB7 | protein | 171 | 9% helix, 52% strand | P34087 |
| H | DNA-directed RNA polymerases I, II, and III subunit rpabc 3 | protein | 134 | 0% helix, 48% strand | P20436 |
| I | DNA-directed RNA polymerase II subunit RPB9 | protein | 119 | 0% helix, 30% strand | P27999 |
| J | DNA-directed RNA polymerases I, II, and III subunit rpabc 5 | protein | 65 | 46% helix, 2% strand | P22139 |
| K | DNA-directed RNA polymerase II subunit RPB11 | protein | 114 | 37% helix, 24% strand | P38902 |
| L | DNA-directed RNA polymerases I, II, and III subunit rpabc 4 | protein | 44 | 0% helix, 20% strand | P40422 |
| M | Transcription initiation factor iib | protein | 189 | 33% helix, 11% strand | P29055 |
| N | 5'-D(*GP*GP*CP*AP*CP*AP*AP*CP*TP*GP*CP*GP*CP*TP)-3' | dna | 7 | — | — |
| P | 5'-R(*AP*UP*AP*UP*CP*AP)-3' | rna | 6 | — | — |
| T | 5'-D(*AP*GP*CP*GP*CP*AP*GP*TP*TP*GP*TP*GP*CP*TP *AP*TP*GP*AP*TP*AP*TP*TP*TP*TP*TP*AP*TP)-3' | dna | 17 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 9 copies · chains A, B, C, I, J, L, M
- MG · Magnesium ion · metal · 2 copies · chains A, P, 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 | 952 | 0.88 | 0.90 | 111 | empty |
| 2 | 748 | 0.88 | 0.92 | 83 | empty |
| 3 | 1101 | 0.84 | 0.85 | 111 | empty |
| 4 | 526 | 0.84 | 0.90 | 79 | empty |
| 5 | 607 | 0.81 | 0.86 | 59 | empty |
Interfaces
39 interfaces between chains.
- A–B · 9724 Ų buried · 147 hydrogen bonds · protein-protein
- A–M · 2648 Ų buried · 50 hydrogen bonds · protein-protein
- D–G · 2459 Ų buried · 31 hydrogen bonds · protein-protein
- A–E · 2205 Ų buried · 26 hydrogen bonds · protein-protein
- C–K · 2160 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 4BBS · Structure of an initially transcribing RNA polymerase II-TFIIB complex · the same entry in another collection · chain T against T, 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 P29055
- Elsewhere: RCSB PDB 4BBS · PDBe 4BBS · 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 P29055
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