MolNFT v1 · #138585 · protein + RNA
Crystal structure of 30S ribosomal subunit from thermus thermophilus
5WNT · 16S ribosomal RNA rRNA: “Crystal structure of 30S ribosomal subunit from thermus thermophilus”. X-ray diffraction, 4 ligands (B6M, MG, K), 20 pockets (best druggability 0.88). MolNFT v1 #138585 on GenesisL1: 3D structure, binding…
- PDB
- 5WNT
- Type
- protein + RNA
- Length
- 3,917 residues
- Chains
- 23
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 16S ribosomal RNA rRNA; Ribosomal protein S2; Ribosomal protein S3; Ribosomal protein S4…
- UniProt
- P80371, P80372, P80373, Q5SHQ5, Q5SLP8, P17291, P0DOY9, P80374, Q5SHN7, P80376, Q5SHN3, P80377, P0DOY6, Q5SJ76, Q5SJH3, P0DOY7, Q5SLQ0, Q5SHP2, P80380, Q5SIH3
- Ligands
- B6M, MG, K, ZN
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 23 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 16S ribosomal RNA rRNA | rna | 1512 | — | — |
| B | Ribosomal protein S2 | protein | 235 | 46% helix, 14% strand | P80371 |
| C | Ribosomal protein S3 | protein | 206 | 38% helix, 23% strand | P80372 |
| D | Ribosomal protein S4 | protein | 208 | 39% helix, 9% strand | P80373 |
| E | Ribosomal protein S5 | protein | 150 | 29% helix, 41% strand | Q5SHQ5 |
| F | Ribosomal protein S6 | protein | 101 | 29% helix, 49% strand | Q5SLP8 |
| G | Ribosomal protein S7 | protein | 155 | 54% helix, 10% strand | P17291 |
| H | Ribosomal protein S8 | protein | 138 | 30% helix, 33% strand | P0DOY9 |
| I | Ribosomal protein S9 | protein | 127 | 34% helix, 20% strand | P80374 |
| J | Ribosomal protein S10 | protein | 98 | 19% helix, 26% strand | Q5SHN7 |
| K | Ribosomal protein S11 | protein | 119 | 28% helix, 29% strand | P80376 |
| L | Ribosomal protein S12 | protein | 124 | 7% helix, 27% strand | Q5SHN3 |
| M | Ribosomal protein S13 | protein | 118 | 50% helix, 2% strand | P80377 |
| N | Ribosomal protein S14 | protein | 60 | 25% helix, 8% strand | P0DOY6 |
| O | Ribosomal protein S15 | protein | 88 | 75% helix, 0% strand | Q5SJ76 |
| P | Ribosomal protein S16 | protein | 83 | 23% helix, 33% strand | Q5SJH3 |
| Q | Ribosomal protein S17 | protein | 99 | 16% helix, 52% strand | P0DOY7 |
| R | Ribosomal protein S18 | protein | 73 | 37% helix, 8% strand | Q5SLQ0 |
| S | Ribosomal protein S19 | protein | 80 | 29% helix, 19% strand | Q5SHP2 |
| T | Ribosomal protein S20 | protein | 99 | 72% helix, 0% strand | P80380 |
| U | Ribosomal protein thx | protein | 24 | 29% helix, 8% strand | Q5SIH3 |
| a | RNA (5'-R(*(A2M)P*AP*AP*UP*U)-3') | rna | 5 | — | — |
| b | RNA (5'-R(P*UP*AP*GP*AP*CP*UP*(70U)P*UP*UP*(12A)P*AP*(PSU) P*CP*UP*A)-3') | rna | 15 | — | — |
Ligands and binding sites
- B6M · (1R,2S,3S,4R,6R)-4,6-diamino-2-{[3-O-(2,6-diamino-2,6-dideoxy-alpha-L-altropyranosyl)-beta-L-arabinofuranosyl]oxy}-3-hydroxycyclohexyl 2-amino-2-deoxy-alpha-D-allopyranoside · ligand · chains A
- MG · Magnesium ion · metal · 252 copies · chains A, D, E, Q, K, T, b, N, a, U, I, L, P, J, M, F, G, H, S
- K · Potassium ion · metal · 22 copies · chains A, Q, E
- 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 | 1059 | 0.88 | 0.91 | 87 | MG |
| 2 | 1079 | 0.86 | 0.87 | 86 | MG |
| 3 | 882 | 0.85 | 0.87 | 91 | MG |
| 4 | 1072 | 0.84 | 0.86 | 73 | MG, K |
| 5 | 895 | 0.84 | 0.87 | 73 | MG, K |
Interfaces
45 interfaces between chains.
- A–L · 3501 Ų buried · 84 hydrogen bonds · protein-nucleic
- A–D · 3173 Ų buried · 98 hydrogen bonds · protein-nucleic
- A–I · 3014 Ų buried · 83 hydrogen bonds · protein-nucleic
- A–T · 2726 Ų buried · 61 hydrogen bonds · protein-nucleic
- A–Q · 2701 Ų buried · 58 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 19 modified (nucleotide modification, nonstandard).
Compared structures
- 5WNT · Crystal Structure of 30S ribosomal subunit from Thermus thermophilus · 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 P0DOY9
- Every structure of UniProt P80374
- Every structure of UniProt Q5SHN7
- Every structure of UniProt P80376
- Every structure of UniProt Q5SHN3
- Every structure of UniProt P80377
- Every structure of UniProt P0DOY6
- Every structure of UniProt Q5SJ76
- Every structure of UniProt Q5SJH3
- Every structure of UniProt P0DOY7
- Every structure of UniProt Q5SLQ0
- Every structure of UniProt Q5SHP2
- Every structure of UniProt P80380
- Every structure of UniProt Q5SIH3
- Elsewhere: RCSB PDB 5WNT · PDBe 5WNT · UniProt P80371 · UniProt P80372 · UniProt P80373 · UniProt Q5SHQ5 · UniProt Q5SLP8 · UniProt P17291 · UniProt P0DOY9 · UniProt P80374 · UniProt Q5SHN7 · UniProt P80376 · UniProt Q5SHN3 · UniProt P80377 · UniProt P0DOY6 · UniProt Q5SJ76 · UniProt Q5SJH3 · UniProt P0DOY7 · UniProt Q5SLQ0 · UniProt Q5SHP2 · UniProt P80380 · UniProt Q5SIH3
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