MolNFT v1 · #89506 · protein + RNA
Crystal structure of the thermus thermophilus (HB8) 30S ribosomal subunit with codon, near-cognate transfer RNA anticodon stem-loop mismatched at the first codon position and streptomycin bound
4DR6 · 16S rRNA: “Crystal structure of the thermus thermophilus (HB8) 30S ribosomal subunit with codon, near-cognate transfer…”. X-ray diffraction, 3 ligands (SRY, MG, ZN), 20 pockets (best druggability 0.88). MolNFT v1 #89506 on…
- PDB
- 4DR6
- Type
- protein + RNA
- Length
- 3,922 residues
- Chains
- 25
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 16S rRNA; 30S ribosomal protein S2; 30S ribosomal protein S3; 30S ribosomal protein S4…
- UniProt
- P80371, P80372, P80373, Q5SHQ5, Q5SLP8, P17291, Q5SHQ2, P80374, Q5SHN7, P80376, F6DEQ7, P80377, Q5SHQ1, Q5SJ76, Q5SJH3, Q5SHP7, Q5SLQ0, Q5SHP2, P80380, Q5SIH3
- Ligands
- SRY, MG, ZN
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 25 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 16S rRNA | rna | 1514 | — | — |
| B | 30S ribosomal protein S2 | protein | 235 | 49% helix, 12% strand | P80371 |
| C | 30S ribosomal protein S3 | protein | 206 | 39% helix, 23% strand | P80372 |
| D | 30S ribosomal protein S4 | protein | 208 | 40% helix, 9% strand | P80373 |
| E | 30S ribosomal protein S5 | protein | 150 | 31% helix, 41% strand | Q5SHQ5 |
| F | 30S ribosomal protein S6 | protein | 101 | 28% helix, 49% strand | Q5SLP8 |
| G | 30S ribosomal protein S7 | protein | 155 | 54% helix, 12% strand | P17291 |
| H | 30S ribosomal protein S8 | protein | 138 | 24% helix, 33% strand | Q5SHQ2 |
| I | 30S ribosomal protein S9 | protein | 127 | 32% helix, 23% strand | P80374 |
| J | 30S ribosomal protein S10 | protein | 98 | 19% helix, 30% strand | Q5SHN7 |
| K | 30S ribosomal protein S11 | protein | 117 | 26% helix, 28% strand | P80376 |
| L | 30S ribosomal protein S12 | protein | 124 | 8% helix, 27% strand | F6DEQ7 |
| M | 30S ribosomal protein S13 | protein | 118 | 51% helix, 2% strand | P80377 |
| N | 30S ribosomal protein S14 | protein | 60 | 25% helix, 7% strand | Q5SHQ1 |
| O | 30S ribosomal protein S15 | protein | 88 | 75% helix, 0% strand | Q5SJ76 |
| P | 30S ribosomal protein S16 | protein | 83 | 22% helix, 30% strand | Q5SJH3 |
| Q | 30S ribosomal protein S17 | protein | 100 | 16% helix, 51% strand | Q5SHP7 |
| R | 30S ribosomal protein S18 | protein | 71 | 38% helix, 8% strand | Q5SLQ0 |
| S | 30S ribosomal protein S19 | protein | 80 | 26% helix, 18% strand | Q5SHP2 |
| T | 30S ribosomal protein S20 | protein | 99 | 73% helix, 0% strand | P80380 |
| U | 30S ribosomal protein thx | protein | 24 | 25% helix, 8% strand | Q5SIH3 |
| V | 5'-R(*UP*UP*UP*U)-3' | rna | 4 | — | — |
| W | 5'-R(P*UP*UP*GP*AP*GP*GP*(PSU)P*GP*G)-3' | rna | 9 | — | — |
| a | 5'-R(P*CP*UP*UP*GP*AP*GP*GP*(PSU)P*GP*GP*U)-3' | rna | 11 | — | — |
| b | 5'-R(*UP*UP*U)-3' | rna | 2 | — | — |
Ligands and binding sites
- SRY · Streptomycin · ligand · chains A, L
- MG · Magnesium ion · metal · 376 copies · chains A, L, Q, E, C, T, N, U, M, G, V, J, I, K, D, F, P, S
- ZN · Zinc ion · metal · 2 copies · chains D, N
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 | 1166 | 0.88 | 0.91 | 96 | MG |
| 2 | 1032 | 0.85 | 0.87 | 87 | MG |
| 3 | 772 | 0.85 | 0.89 | 80 | MG |
| 4 | 836 | 0.84 | 0.88 | 66 | MG |
| 5 | 794 | 0.83 | 0.87 | 58 | MG |
Interfaces
46 interfaces between chains.
- A–L · 3360 Ų buried · 85 hydrogen bonds · protein-nucleic
- A–D · 3071 Ų buried · 87 hydrogen bonds · protein-nucleic
- A–I · 3023 Ų buried · 67 hydrogen bonds · protein-nucleic
- A–Q · 2683 Ų buried · 58 hydrogen bonds · protein-nucleic
- A–T · 2582 Ų buried · 63 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 17 modified (nucleotide modification, nonstandard).
Compared structures
- 4DR6 · Crystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with codon… · 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 P80371
- Every structure of UniProt P80372
- Every structure of UniProt P80373
- Every structure of UniProt Q5SHQ5
- Every structure of UniProt Q5SLP8
- Every structure of UniProt P17291
- Every structure of UniProt Q5SHQ2
- Every structure of UniProt P80374
- Every structure of UniProt Q5SHN7
- Every structure of UniProt P80376
- Every structure of UniProt F6DEQ7
- Every structure of UniProt P80377
- Every structure of UniProt Q5SHQ1
- Every structure of UniProt Q5SJ76
- Every structure of UniProt Q5SJH3
- Every structure of UniProt Q5SHP7
- Every structure of UniProt Q5SLQ0
- Every structure of UniProt Q5SHP2
- Every structure of UniProt P80380
- Every structure of UniProt Q5SIH3
- Elsewhere: RCSB PDB 4DR6 · PDBe 4DR6 · UniProt P80371 · UniProt P80372 · UniProt P80373 · UniProt Q5SHQ5 · UniProt Q5SLP8 · UniProt P17291 · UniProt Q5SHQ2 · UniProt P80374 · UniProt Q5SHN7 · UniProt P80376 · UniProt F6DEQ7 · UniProt P80377 · UniProt Q5SHQ1 · UniProt Q5SJ76 · UniProt Q5SJH3 · UniProt Q5SHP7 · UniProt Q5SLQ0 · UniProt Q5SHP2 · UniProt P80380 · UniProt Q5SIH3
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