MolNFT v1 · #146076 · protein + RNA
Human nuclear exosome-MTR4 RNA complex - overall reconstruction
6D6Q · Exosome complex component RRP45: “Human nuclear exosome-MTR4 RNA complex - overall reconstruction”. Electron microscopy, 3 ligands (ANP, MG, ZN), 20 pockets (best druggability 0.86). MolNFT v1 #146076 on GenesisL1: 3D structure…
- PDB
- 6D6Q
- Type
- protein + RNA
- Length
- 3,950 residues
- Chains
- 15
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exosome complex component RRP45; Exosome complex component RRP41; Exosome complex…
- EC
- 3.1.13.-, 3.1.26.-, 3.6.4.13
- UniProt
- Q06265, Q9NPD3, Q96B26, Q9NQT4, Q15024, Q5RKV6, Q9NQT5, Q13868, Q9Y3B2, Q01780, Q9Y2L1, Q99547, P42285
- Ligands
- ANP, MG, ZN
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 15 distinct chains · 30% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exosome complex component RRP45 | protein | 287 | 29% helix, 32% strand | Q06265 |
| B | Exosome complex component RRP41 | protein | 241 | 31% helix, 28% strand | Q9NPD3 |
| C | Exosome complex component RRP43 | protein | 265 | 28% helix, 33% strand | Q96B26 |
| D | Exosome complex component RRP46 | protein | 208 | 31% helix, 34% strand | Q9NQT4 |
| E | Exosome complex component RRP42 | protein | 286 | 28% helix, 30% strand | Q15024 |
| F | Exosome complex component MTR3 | protein | 252 | 28% helix, 25% strand | Q5RKV6 |
| G | Exosome complex component RRP40 | protein | 237 | 16% helix, 31% strand | Q9NQT5 |
| H | Exosome complex component RRP4 | protein | 289 | 22% helix, 26% strand | Q13868 |
| I | Exosome complex component CSL4 | protein | 183 | 5% helix, 44% strand | Q9Y3B2 |
| J | Exosome component 10 (EC 3.1.13.-) | protein | 11 | 0% helix, 9% strand | Q01780 |
| K | Exosome complex exonuclease RRP44 (EC 3.1.13.-, 3.1.26.-) | protein | 853 | 30% helix, 22% strand | Q9Y2L1 |
| L | M-phase phosphoprotein 6 | protein | 68 | 32% helix, 9% strand | Q99547 |
| M | Exosome RNA helicase MTR4 (EC 3.6.4.13) | protein | 709 | 45% helix, 13% strand | P42285 |
| N | RNA (5'-R(*AP*GP*CP*AP*CP*CP*GP*UP*AP*AP*AP*GP*AP*CP*GP*C)- 3') | rna | 13 | — | — |
| O | DNA/RNA (62-mer) | rna | 48 | — | — |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains M
- MG · Magnesium ion · metal · chains K, O
- ZN · Zinc ion · metal · chains K
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 | 880 | 0.86 | 0.88 | 76 | empty |
| 2 | 920 | 0.86 | 0.87 | 105 | empty |
| 3 | 1117 | 0.85 | 0.86 | 95 | empty |
| 4 | 1074 | 0.84 | 0.85 | 116 | empty |
| 5 | 830 | 0.82 | 0.84 | 107 | empty |
Interfaces
35 interfaces between chains.
- K–O · 2506 Ų buried · 53 hydrogen bonds · protein-nucleic
- C–F · 1928 Ų buried · 13 hydrogen bonds · protein-protein
- G–L · 1876 Ų buried · 19 hydrogen bonds · protein-protein
- E–H · 1706 Ų buried · 9 hydrogen bonds · protein-protein
- B–H · 1618 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6D6Q · Human nuclear exosome-MTR4 RNA complex - overall reconstruction · 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 Q06265
- Every structure of UniProt Q9NPD3
- Every structure of UniProt Q96B26
- Every structure of UniProt Q9NQT4
- Every structure of UniProt Q15024
- Every structure of UniProt Q5RKV6
- Every structure of UniProt Q9NQT5
- Every structure of UniProt Q13868
- Every structure of UniProt Q9Y3B2
- Every structure of UniProt Q01780
- Every structure of UniProt Q9Y2L1
- Every structure of UniProt Q99547
- Every structure of UniProt P42285
- Elsewhere: RCSB PDB 6D6Q · PDBe 6D6Q · UniProt Q06265 · UniProt Q9NPD3 · UniProt Q96B26 · UniProt Q9NQT4 · UniProt Q15024 · UniProt Q5RKV6 · UniProt Q9NQT5 · UniProt Q13868 · UniProt Q9Y3B2 · UniProt Q01780 · UniProt Q9Y2L1 · UniProt Q99547 · UniProt P42285
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