MolNFT v1 · #147007 · protein + RNA
Cryo-EM structure of mycobacterium smegmatis C(MINUS) 30S ribosomal subunit with mpy
6DZK · 16S rRNA: “Cryo-EM structure of mycobacterium smegmatis C(MINUS) 30S ribosomal subunit with mpy”. Electron microscopy, 20 pockets (best druggability 0.86). MolNFT v1 #147007 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6DZK
- Type
- protein + RNA
- Length
- 4,079 residues
- Chains
- 23
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 16S rRNA; Conserved domain protein; 30S ribosomal protein S3; 30S ribosomal protein S4…
- UniProt
- A0QSD7, A0QSL7, A0QSG6, A0A0D6J3X3, A0QS97, A0QSG3, A0QSP9, A0QSD0, A0QSL6, A0QS96, A0QSL5, A0QVQ3, A0QV37, A0QSE0, A0QSD5, A0R102, A0QVB8, A0R549, A0QTK6, A0R550, A0R554
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 23 distinct chains · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 16S rRNA | rna | 1511 | — | — |
| B | Conserved domain protein | protein | 32 | 78% helix, 0% strand | — |
| C | 30S ribosomal protein S3 | protein | 208 | 30% helix, 22% strand | A0QSD7 |
| D | 30S ribosomal protein S4 | protein | 200 | 46% helix, 9% strand | A0QSL7 |
| E | 30S ribosomal protein S5 | protein | 180 | 38% helix, 27% strand | A0QSG6 |
| F | 30S ribosomal protein S6 | protein | 96 | 33% helix, 33% strand | A0A0D6J3X3 |
| G | 30S ribosomal protein S7 | protein | 155 | 57% helix, 5% strand | A0QS97 |
| H | 30S ribosomal protein S8 | protein | 131 | 31% helix, 29% strand | A0QSG3 |
| I | 30S ribosomal protein S9 | protein | 126 | 31% helix, 15% strand | A0QSP9 |
| J | 30S ribosomal protein S10 | protein | 99 | 24% helix, 40% strand | A0QSD0 |
| K | 30S ribosomal protein S11 | protein | 115 | 28% helix, 26% strand | A0QSL6 |
| L | 30S ribosomal protein S12 | protein | 122 | 5% helix, 27% strand | A0QS96 |
| M | 30S ribosomal protein S13 | protein | 116 | 53% helix, 0% strand | A0QSL5 |
| O | 30S ribosomal protein S15 | protein | 88 | 75% helix, 0% strand | A0QVQ3 |
| P | 30S ribosomal protein S16 | protein | 113 | 33% helix, 20% strand | A0QV37 |
| Q | 30S ribosomal protein S17 | protein | 94 | 0% helix, 54% strand | A0QSE0 |
| S | 30S ribosomal protein S19 | protein | 82 | 26% helix, 18% strand | A0QSD5 |
| T | 30S ribosomal protein S20 | protein | 85 | 87% helix, 0% strand | A0R102 |
| V | 30S ribosomal protein S2 | protein | 228 | 46% helix, 3% strand | A0QVB8 |
| r | 30S ribosomal protein S18 1 | protein | 84 | 32% helix, 2% strand | A0R549 |
| Y | Ribosome hibernation promoting factor | protein | 103 | 36% helix, 22% strand | A0QTK6 |
| N | 30S ribosomal protein S14 | protein | 100 | 43% helix, 4% strand | A0R550 |
| g | 50S ribosomal protein L31 | protein | 11 | 64% helix, 0% strand | A0R554 |
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 | 605 | 0.86 | 0.92 | 65 | empty |
| 2 | 841 | 0.86 | 0.90 | 65 | empty |
| 3 | 942 | 0.85 | 0.88 | 88 | empty |
| 4 | 1168 | 0.85 | 0.86 | 96 | empty |
| 5 | 595 | 0.84 | 0.90 | 65 | empty |
Interfaces
46 interfaces between chains.
- A–L · 3025 Ų buried · 85 hydrogen bonds · protein-nucleic
- A–I · 2907 Ų buried · 61 hydrogen bonds · protein-nucleic
- A–D · 2887 Ų buried · 64 hydrogen bonds · protein-nucleic
- A–Q · 2546 Ų buried · 52 hydrogen bonds · protein-nucleic
- A–N · 2497 Ų buried · 53 hydrogen bonds · protein-nucleic
Compared structures
- 6DZK · Cryo-EM Structure of Mycobacterium smegmatis C(minus) 30S ribosomal subunit with MPY · 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 A0QSD7
- Every structure of UniProt A0QSL7
- Every structure of UniProt A0QSG6
- Every structure of UniProt A0A0D6J3X3
- Every structure of UniProt A0QS97
- Every structure of UniProt A0QSG3
- Every structure of UniProt A0QSP9
- Every structure of UniProt A0QSD0
- Every structure of UniProt A0QSL6
- Every structure of UniProt A0QS96
- Every structure of UniProt A0QSL5
- Every structure of UniProt A0QVQ3
- Every structure of UniProt A0QV37
- Every structure of UniProt A0QSE0
- Every structure of UniProt A0QSD5
- Every structure of UniProt A0R102
- Every structure of UniProt A0QVB8
- Every structure of UniProt A0R549
- Every structure of UniProt A0QTK6
- Every structure of UniProt A0R550
- Every structure of UniProt A0R554
- Elsewhere: RCSB PDB 6DZK · PDBe 6DZK · UniProt A0QSD7 · UniProt A0QSL7 · UniProt A0QSG6 · UniProt A0A0D6J3X3 · UniProt A0QS97 · UniProt A0QSG3 · UniProt A0QSP9 · UniProt A0QSD0 · UniProt A0QSL6 · UniProt A0QS96 · UniProt A0QSL5 · UniProt A0QVQ3 · UniProt A0QV37 · UniProt A0QSE0 · UniProt A0QSD5 · UniProt A0R102 · UniProt A0QVB8 · UniProt A0R549 · UniProt A0QTK6 · UniProt A0R550 · UniProt A0R554
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