MolNFT v1 · #183297 · protein + DNA + RNA
RNA polymerase II-SPT4/5-nucleosome-fact structure
7NKY · RNA (5'- R(P*UP*CP*UP*UP*UP*UP*AP*UP*UP*UP*UP*UP*UP*CP*UP*G)…: “RNA polymerase II-SPT4/5-nucleosome-fact structure”. Electron microscopy, 2 ligands (ZN, MG), 20 pockets (best druggability 0.90). MolNFT v1 #183297 on GenesisL1: 3D…
- PDB
- 7NKY
- Type
- protein + DNA + RNA
- Length
- 6,035 residues
- Chains
- 27
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'- R(P*UP*CP*UP*UP*UP*UP*AP*UP*UP*UP*UP*UP*UP*CP*UP*G)-3'); DNA (138-mer); DNA…
- EC
- 2.7.7.6
- UniProt
- P04050, P08518, P16370, P20434, P20435, P20436, P27999, P22139, P38902, P40422, A0A6A5PX04, A0A6L0ZFJ2, P20433, P34087, A0A6A5PUM6, P32558, P84233, P62799, P06897, P02281
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.90
Structure
electron microscopy · 27 distinct chains · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | RNA (5'- R(P*UP*CP*UP*UP*UP*UP*AP*UP*UP*UP*UP*UP*UP*CP*UP*G)-3') | rna | 16 | — | — |
| N | DNA (138-mer) | dna | 138 | — | — |
| T | DNA (148-mer) | dna | 148 | — | — |
| A | DNA-directed RNA polymerase II subunit RPB1 (EC 2.7.7.6) | protein | 1410 | 42% helix, 15% strand | P04050 |
| B | DNA-directed RNA polymerase II subunit RPB2 (EC 2.7.7.6) | protein | 1116 | 29% helix, 24% strand | P08518 |
| C | DNA-directed RNA polymerase II subunit RPB3 | protein | 265 | 24% helix, 29% strand | P16370 |
| E | DNA-directed RNA polymerases I, II, and III subunit RPABC1 | protein | 214 | 37% helix, 20% strand | P20434 |
| F | DNA-directed RNA polymerases I, II, and III subunit RPABC2 | protein | 87 | 34% helix, 15% strand | P20435 |
| H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | protein | 133 | 4% helix, 49% strand | P20436 |
| I | DNA-directed RNA polymerase II subunit RPB9 | protein | 119 | 3% helix, 26% strand | P27999 |
| J | DNA-directed RNA polymerases I, II, and III subunit RPABC5 | protein | 65 | 51% helix, 5% strand | P22139 |
| K | DNA-directed RNA polymerase II subunit RPB11 | protein | 114 | 38% helix, 24% strand | P38902 |
| L | DNA-directed RNA polymerases I, II, and III subunit RPABC4 | protein | 44 | 0% helix, 16% strand | P40422 |
| Y | Chromatin elongation factor SPT4 | protein | 98 | 29% helix, 24% strand | A0A6A5PX04 |
| Z | Transcription elongation factor SPT5 | protein | 156 | 21% helix, 29% strand | A0A6L0ZFJ2 |
| D | DNA-directed RNA polymerase II subunit RPB4 | protein | 180 | 52% helix, 5% strand | P20433 |
| G | DNA-directed RNA polymerase II subunit RPB7 | protein | 171 | 13% helix, 49% strand | P34087 |
| O | Fact complex subunit POB3 | protein | 427 | 12% helix, 39% strand | A0A6A5PUM6 |
| Q | Fact complex subunit SPT16 | protein | 404 | 19% helix, 29% strand | P32558 |
| a | Histone H3.2 | protein | 88 | 75% helix, 2% strand | P84233 |
| b | Histone H4 | protein | 83 | 58% helix, 5% strand | P62799 |
| c | Histone H2A type 1 | protein | 102 | 59% helix, 5% strand | P06897 |
| d | Histone H2B 1.1 | protein | 95 | 74% helix, 3% strand | P02281 |
| e | Histone H3.2 | protein | 94 | 70% helix, 3% strand | P84233 |
| f | Histone H4 | protein | 78 | 68% helix, 6% strand | P62799 |
| g | Histone H2A type 1 | protein | 97 | 61% helix, 4% strand | P06897 |
| h | Histone H2B 1.1 | protein | 93 | 75% helix, 2% strand | P02281 |
Ligands and binding sites
- ZN · Zinc ion · metal · 9 copies · chains A, B, C, Z, I, J, L, Y
- MG · Magnesium ion · metal · chains P, A
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 | 1164 | 0.90 | 0.92 | 166 | empty |
| 2 | 932 | 0.85 | 0.87 | 117 | empty |
| 3 | 792 | 0.83 | 0.86 | 86 | empty |
| 4 | 689 | 0.81 | 0.86 | 74 | empty |
| 5 | 669 | 0.81 | 0.85 | 68 | empty |
Interfaces
90 interfaces between chains.
- A–B · 9925 Ų buried · 130 hydrogen bonds · protein-protein
- N–T · 6270 Ų buried · 467 hydrogen bonds · nucleic-nucleic
- O–Q · 2992 Ų buried · 60 hydrogen bonds · protein-protein
- g–h · 2647 Ų buried · 26 hydrogen bonds · protein-protein
- c–d · 2578 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 7NKY · RNA Polymerase II-Spt4/5-nucleosome-FACT structure · 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 P04050
- Every structure of UniProt P08518
- Every structure of UniProt P16370
- Every structure of UniProt P20434
- Every structure of UniProt P20435
- 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 A0A6A5PX04
- Every structure of UniProt A0A6L0ZFJ2
- Every structure of UniProt P20433
- Every structure of UniProt P34087
- Every structure of UniProt A0A6A5PUM6
- Every structure of UniProt P32558
- Every structure of UniProt P84233
- Every structure of UniProt P62799
- Every structure of UniProt P06897
- Every structure of UniProt P02281
- Elsewhere: RCSB PDB 7NKY · PDBe 7NKY · UniProt P04050 · UniProt P08518 · UniProt P16370 · UniProt P20434 · UniProt P20435 · UniProt P20436 · UniProt P27999 · UniProt P22139 · UniProt P38902 · UniProt P40422 · UniProt A0A6A5PX04 · UniProt A0A6L0ZFJ2 · UniProt P20433 · UniProt P34087 · UniProt A0A6A5PUM6 · UniProt P32558 · UniProt P84233 · UniProt P62799 · UniProt P06897 · UniProt P02281
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