MolNFT v1 · #139731 · protein + DNA + RNA
RNA polymerase II elongation complex bound with SPT5 KOW5 and ELF1
5XOG · DNA-directed RNA polymerase subunit: “RNA polymerase II elongation complex bound with SPT5 KOW5 and ELF1”. X-ray diffraction, 3 ligands (APC, ZN, MG), 20 pockets (best druggability 0.87). MolNFT v1 #139731 on GenesisL1: 3D…
- PDB
- 5XOG
- Type
- protein + DNA + RNA
- Length
- 4,131 residues
- Chains
- 17
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase subunit; DNA-directed RNA polymerase subunit beta; RNA…
- EC
- 2.7.7.6
- UniProt
- C4R4Y0, C4QZQ7, C4R7L2, C4R2U9, C4R3P8, C4R1V1, C4R9A1, C4R273, F2QPE6, C4R009, C4R3Z5, F2QMI1, A0A1B2JER8, F2QUC3
- Ligands
- APC, ZN, MG
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 17 distinct chains · 32% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit (EC 2.7.7.6) | protein | 1414 | 42% helix, 17% strand | C4R4Y0 |
| B | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1161 | 27% helix, 25% strand | C4QZQ7 |
| C | RNA polymerase II third largest subunit B44, part of central core | protein | 263 | 25% helix, 29% strand | C4R7L2 |
| D | RNA polymerase II subunit B32 | protein | 168 | 51% helix, 8% strand | C4R2U9 |
| E | RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III | protein | 213 | 40% helix, 23% strand | C4R3P8 |
| F | RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III | protein | 84 | 35% helix, 17% strand | C4R1V1 |
| G | RNA polymerase II subunit | protein | 171 | 13% helix, 49% strand | C4R9A1 |
| H | RNA polymerase subunit ABC14.5, common to RNA polymerases I, II, and III | protein | 133 | 8% helix, 50% strand | C4R273 |
| I | DNA-directed RNA polymerase subunit | protein | 111 | 3% helix, 32% strand | F2QPE6 |
| J | RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III | protein | 66 | 44% helix, 5% strand | C4R009 |
| K | RNA polymerase II subunit B12.5 | protein | 113 | 41% helix, 24% strand | C4R3Z5 |
| L | RNA polymerase subunit ABC10-alpha | protein | 45 | 0% helix, 36% strand | F2QMI1 |
| P | RNA (5'- R(*UP*UP*UP*UP*UP*UP*UP*AP*UP*CP*GP*AP*GP*AP*GP*GP*U)-3') | rna | 11 | — | — |
| T | DNA (39-mer) | dna | 32 | — | — |
| N | DNA (30-mer) | dna | 21 | — | — |
| M | Transcription elongation factor 1 homolog | protein | 64 | 19% helix, 36% strand | A0A1B2JER8 |
| W | SPT4/5 complex component | protein | 61 | 5% helix, 44% strand | F2QUC3 |
Ligands and binding sites
- APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · chains A, B, P, T
- ZN · Zinc ion · metal · 9 copies · chains A, B, C, I, J, L, M
- MG · Magnesium ion · metal · chains A, P
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 | 536 | 0.87 | 0.93 | 75 | empty |
| 2 | 1009 | 0.85 | 0.86 | 91 | empty |
| 3 | 945 | 0.84 | 0.86 | 89 | empty |
| 4 | 375 | 0.82 | 0.90 | 41 | empty |
| 5 | 1124 | 0.82 | 0.83 | 113 | empty |
Interfaces
44 interfaces between chains.
- A–B · 10077 Ų buried · 142 hydrogen bonds · protein-protein
- D–G · 2323 Ų buried · 25 hydrogen bonds · protein-protein
- A–E · 2276 Ų buried · 29 hydrogen bonds · protein-protein
- C–K · 2076 Ų buried · 18 hydrogen bonds · protein-protein
- A–F · 2046 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5XOG · RNA Polymerase II elongation complex bound with Spt5 KOW5 and Elf1 · the same entry in another collection · chain A against A, 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 C4R4Y0
- Every structure of UniProt C4QZQ7
- Every structure of UniProt C4R7L2
- Every structure of UniProt C4R2U9
- Every structure of UniProt C4R3P8
- Every structure of UniProt C4R1V1
- Every structure of UniProt C4R9A1
- Every structure of UniProt C4R273
- Every structure of UniProt F2QPE6
- Every structure of UniProt C4R009
- Every structure of UniProt C4R3Z5
- Every structure of UniProt F2QMI1
- Every structure of UniProt A0A1B2JER8
- Every structure of UniProt F2QUC3
- Elsewhere: RCSB PDB 5XOG · PDBe 5XOG · UniProt C4R4Y0 · UniProt C4QZQ7 · UniProt C4R7L2 · UniProt C4R2U9 · UniProt C4R3P8 · UniProt C4R1V1 · UniProt C4R9A1 · UniProt C4R273 · UniProt F2QPE6 · UniProt C4R009 · UniProt C4R3Z5 · UniProt F2QMI1 · UniProt A0A1B2JER8 · UniProt F2QUC3
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