MolNFT v1 · #127488 · protein + RNA
E. COLI expressome
5MY1 · 16S ribosomal RNA: “E. COLI expressome”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.88). MolNFT v1 #127488 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5MY1
- Type
- protein + RNA
- Length
- 7,094 residues
- Chains
- 26
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 16S ribosomal RNA; 30S ribosomal protein S3; 30S ribosomal protein S4; 30S ribosomal…
- EC
- 2.7.7.6
- UniProt
- P0A7V3, P0A7V8, P0A7W1, P02358, P02359, P0A7W7, P0A7X3, P0A7R5, P0A7R9, P0A7S3, P0A7S9, P0AG59, P0ADZ4, P0A7T3, P0AG63, P0A7T7, P0A7U3, P0A7U7, P0A7V0, P68679, P0A7Z4, B1XBY9, P0A8T7, B1X982
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 26 distinct chains · 33% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 16S ribosomal RNA | rna | 1530 | — | — |
| C | 30S ribosomal protein S3 | protein | 206 | 32% helix, 16% strand | P0A7V3 |
| D | 30S ribosomal protein S4 | protein | 205 | 37% helix, 8% strand | P0A7V8 |
| E | 30S ribosomal protein S5 | protein | 150 | 25% helix, 27% strand | P0A7W1 |
| F | 30S ribosomal protein S6 | protein | 100 | 31% helix, 23% strand | P02358 |
| G | 30S ribosomal protein S7 | protein | 150 | 49% helix, 1% strand | P02359 |
| H | 30S ribosomal protein S8 | protein | 129 | 29% helix, 29% strand | P0A7W7 |
| I | 30S ribosomal protein S9 | protein | 127 | 28% helix, 12% strand | P0A7X3 |
| J | 30S ribosomal protein S10 | protein | 98 | 15% helix, 21% strand | P0A7R5 |
| K | 30S ribosomal protein S11 | protein | 117 | 19% helix, 15% strand | P0A7R9 |
| L | 30S ribosomal protein S12 | protein | 123 | 5% helix, 14% strand | P0A7S3 |
| M | 30S ribosomal protein S13 | protein | 114 | 42% helix, 2% strand | P0A7S9 |
| N | 30S ribosomal protein S14 | protein | 96 | 42% helix, 4% strand | P0AG59 |
| O | 30S ribosomal protein S15 | protein | 88 | 65% helix, 0% strand | P0ADZ4 |
| P | 30S ribosomal protein S16 | protein | 82 | 21% helix, 16% strand | P0A7T3 |
| Q | 30S ribosomal protein S17 | protein | 80 | 0% helix, 19% strand | P0AG63 |
| R | 30S ribosomal protein S18 | protein | 55 | 33% helix, 0% strand | P0A7T7 |
| S | 30S ribosomal protein S19 | protein | 79 | 20% helix, 5% strand | P0A7U3 |
| T | 30S ribosomal protein S20 | protein | 85 | 78% helix, 0% strand | P0A7U7 |
| B | 30S ribosomal protein S2 | protein | 218 | 43% helix, 6% strand | P0A7V0 |
| U | 30S ribosomal protein S21 | protein | 51 | 41% helix, 0% strand | P68679 |
| V | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 225 | 19% helix, 36% strand | P0A7Z4 |
| W | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 216 | 21% helix, 33% strand | P0A7Z4 |
| X | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1319 | 31% helix, 17% strand | B1XBY9 |
| Y | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1372 | 36% helix, 12% strand | P0A8T7 |
| Z | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 79 | 67% helix, 1% strand | B1X982 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains Y
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 | 813 | 0.88 | 0.91 | 139 | empty |
| 2 | 662 | 0.85 | 0.91 | 56 | empty |
| 3 | 1120 | 0.85 | 0.86 | 93 | empty |
| 4 | 1163 | 0.84 | 0.85 | 92 | empty |
| 5 | 1114 | 0.83 | 0.85 | 96 | empty |
Interfaces
56 interfaces between chains.
- X–Y · 5291 Ų buried · 36 hydrogen bonds · protein-protein
- A–D · 2939 Ų buried · 64 hydrogen bonds · protein-nucleic
- A–I · 2874 Ų buried · 81 hydrogen bonds · protein-nucleic
- A–L · 2682 Ų buried · 69 hydrogen bonds · protein-nucleic
- A–T · 2237 Ų buried · 46 hydrogen bonds · protein-nucleic
Compared structures
- 5MY1 · E. coli expressome · the same entry in another collection · chain M against M, 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 P0A7V3
- Every structure of UniProt P0A7V8
- Every structure of UniProt P0A7W1
- Every structure of UniProt P02358
- Every structure of UniProt P02359
- Every structure of UniProt P0A7W7
- Every structure of UniProt P0A7X3
- Every structure of UniProt P0A7R5
- Every structure of UniProt P0A7R9
- Every structure of UniProt P0A7S3
- Every structure of UniProt P0A7S9
- Every structure of UniProt P0AG59
- Every structure of UniProt P0ADZ4
- Every structure of UniProt P0A7T3
- Every structure of UniProt P0AG63
- Every structure of UniProt P0A7T7
- Every structure of UniProt P0A7U3
- Every structure of UniProt P0A7U7
- Every structure of UniProt P0A7V0
- Every structure of UniProt P68679
- Every structure of UniProt P0A7Z4
- Every structure of UniProt B1XBY9
- Every structure of UniProt P0A8T7
- Every structure of UniProt B1X982
- Elsewhere: RCSB PDB 5MY1 · PDBe 5MY1 · UniProt P0A7V3 · UniProt P0A7V8 · UniProt P0A7W1 · UniProt P02358 · UniProt P02359 · UniProt P0A7W7 · UniProt P0A7X3 · UniProt P0A7R5 · UniProt P0A7R9 · UniProt P0A7S3 · UniProt P0A7S9 · UniProt P0AG59 · UniProt P0ADZ4 · UniProt P0A7T3 · UniProt P0AG63 · UniProt P0A7T7 · UniProt P0A7U3 · UniProt P0A7U7 · UniProt P0A7V0 · UniProt P68679 · UniProt P0A7Z4 · UniProt B1XBY9 · UniProt P0A8T7 · UniProt B1X982
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