Research workbench
Crystal structure of kasugamycin bound to the 30S ribosomal subunit
Analyse Crystal structure of kasugamycin bound to the 30S ribosomal subunit in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2HHH
- Type
- protein + RNA
- Length
- 3,901 residues
- Chains
- 21
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 16S ribosomal RNA; 30S ribosomal protein S2; 30S ribosomal protein S3; 30S ribosomal…
- UniProt
- P80371, P80372, P80373, P27152, P23370, P17291, P24319, P80374, P80375, P80376, P17293, P80377, P24320, P80378, Q5SJH3, P24321, P80382, P80381, P80380, P62612
- Ligands
- KSG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 21 distinct chains · 35% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 16S ribosomal RNA | rna | 1505 | — | — |
| B | 30S ribosomal protein S2 | protein | 234 | 47% helix, 12% strand | P80371 |
| C | 30S ribosomal protein S3 | protein | 206 | 36% helix, 19% strand | P80372 |
| D | 30S ribosomal protein S4 | protein | 208 | 37% helix, 9% strand | P80373 |
| E | 30S ribosomal protein S5 | protein | 150 | 28% helix, 31% strand | P27152 |
| F | 30S ribosomal protein S6 | protein | 101 | 29% helix, 41% strand | P23370 |
| G | 30S ribosomal protein S7 | protein | 155 | 50% helix, 10% strand | P17291 |
| H | 30S ribosomal protein S8 | protein | 138 | 28% helix, 33% strand | P24319 |
| I | 30S ribosomal protein S9 | protein | 127 | 32% helix, 17% strand | P80374 |
| J | 30S ribosomal protein S10 | protein | 98 | 19% helix, 28% strand | P80375 |
| K | 30S ribosomal protein S11 | protein | 119 | 29% helix, 26% strand | P80376 |
| L | 30S ribosomal protein S12 | protein | 124 | 6% helix, 25% strand | P17293 |
| M | 30S ribosomal protein S13 | protein | 125 | 48% helix, 2% strand | P80377 |
| N | 30S ribosomal protein S14 | protein | 60 | 13% helix, 8% strand | P24320 |
| O | 30S ribosomal protein S15 | protein | 88 | 74% helix, 0% strand | P80378 |
| P | 30S ribosomal protein S16 | protein | 83 | 23% helix, 20% strand | Q5SJH3 |
| Q | 30S ribosomal protein S17 | protein | 104 | 13% helix, 43% strand | P24321 |
| R | 30S ribosomal protein S18 | protein | 73 | 34% helix, 5% strand | P80382 |
| S | 30S ribosomal protein S19 | protein | 80 | 26% helix, 19% strand | P80381 |
| T | 30S ribosomal protein S20 | protein | 99 | 70% helix, 0% strand | P80380 |
| U | 30S ribosomal protein thx | protein | 24 | 21% helix, 8% strand | P62612 |
Ligands and binding sites
- KSG · (1S,2R,3S,4R,5S,6S)-2,3,4,5,6-pentahydroxycyclohexyl 2-amino-4-{[carboxy(imino)methyl]amino}-2,3,4,6-tetradeoxy-alpha-D-arabino-hexopyranoside · ligand · 2 copies · chains A, G
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 | 748 | 0.86 | 0.90 | 57 | empty |
| 2 | 913 | 0.84 | 0.87 | 94 | empty |
| 3 | 575 | 0.84 | 0.90 | 58 | empty |
| 4 | 756 | 0.84 | 0.87 | 85 | empty |
| 5 | 1148 | 0.83 | 0.85 | 86 | empty |
Interfaces
42 interfaces between chains.
- A–L · 3270 Ų buried · 101 hydrogen bonds · protein-nucleic
- A–I · 3056 Ų buried · 108 hydrogen bonds · protein-nucleic
- A–D · 2981 Ų buried · 85 hydrogen bonds · protein-nucleic
- A–Q · 2821 Ų buried · 74 hydrogen bonds · protein-nucleic
- A–T · 2649 Ų buried · 76 hydrogen bonds · protein-nucleic
Compared structures
- 2HHH · Crystal structure of kasugamycin bound to the 30S ribosomal subunit · the same entry in another collection · chain K against K, 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 P27152
- Every structure of UniProt P23370
- Every structure of UniProt P17291
- Every structure of UniProt P24319
- Every structure of UniProt P80374
- Every structure of UniProt P80375
- Every structure of UniProt P80376
- Every structure of UniProt P17293
- Every structure of UniProt P80377
- Every structure of UniProt P24320
- Every structure of UniProt P80378
- Every structure of UniProt Q5SJH3
- Every structure of UniProt P24321
- Every structure of UniProt P80382
- Every structure of UniProt P80381
- Every structure of UniProt P80380
- Every structure of UniProt P62612
- Elsewhere: RCSB PDB 2HHH · PDBe 2HHH · UniProt P80371 · UniProt P80372 · UniProt P80373 · UniProt P27152 · UniProt P23370 · UniProt P17291 · UniProt P24319 · UniProt P80374 · UniProt P80375 · UniProt P80376 · UniProt P17293 · UniProt P80377 · UniProt P24320 · UniProt P80378 · UniProt Q5SJH3 · UniProt P24321 · UniProt P80382 · UniProt P80381 · UniProt P80380 · UniProt P62612
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