MolNFT v1 · #171103 · protein + RNA
Acinetobacter baumannii ribosome-tigecycline complex - 30S subunit head
6YTF · 16S ribosomal RNA: “Acinetobacter baumannii ribosome-tigecycline complex - 30S subunit head”. Electron microscopy, 2 ligands (T1C, MG), 20 pockets (best druggability 0.84). MolNFT v1 #171103 on GenesisL1: 3D structure, binding sites…
- PDB
- 6YTF
- Type
- protein + RNA
- Length
- 1,329 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 16S ribosomal RNA; E-site tRNA; MRNA; 30S ribosomal protein S3; 30S ribosomal protein S7…
- UniProt
- D0CD03, D0C9P7, D0CG36, D0CCZ6, D0CD19, D0CD10, D0CD01
- Ligands
- T1C, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 10 distinct chains · 37% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 3 | 16S ribosomal RNA | rna | 453 | — | — |
| 7 | E-site tRNA | rna | 20 | — | — |
| 9 | MRNA | rna | 4 | — | — |
| d | 30S ribosomal protein S3 | protein | 210 | 31% helix, 28% strand | D0CD03 |
| h | 30S ribosomal protein S7 | protein | 117 | 55% helix, 0% strand | D0C9P7 |
| j | 30S ribosomal protein S9 | protein | 127 | 34% helix, 18% strand | D0CG36 |
| k | 30S ribosomal protein S10 | protein | 100 | 22% helix, 45% strand | D0CCZ6 |
| n | 30S ribosomal protein S13 | protein | 115 | 48% helix, 3% strand | D0CD19 |
| o | 30S ribosomal protein S14 | protein | 100 | 52% helix, 4% strand | D0CD10 |
| t | 30S ribosomal protein S19 | protein | 83 | 20% helix, 18% strand | D0CD01 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1197 | 0.84 | 0.86 | 90 | MG |
| 2 | 821 | 0.84 | 0.88 | 62 | MG |
| 3 | 982 | 0.83 | 0.85 | 98 | MG |
| 4 | 646 | 0.82 | 0.88 | 76 | MG |
| 5 | 922 | 0.81 | 0.83 | 73 | MG |
Interfaces
19 interfaces between chains.
- 3–j · 2824 Ų buried · 64 hydrogen bonds · protein-nucleic
- 3–o · 2300 Ų buried · 54 hydrogen bonds · protein-nucleic
- 3–n · 1968 Ų buried · 42 hydrogen bonds · protein-nucleic
- 3–k · 1736 Ų buried · 43 hydrogen bonds · protein-nucleic
- 3–d · 1648 Ų buried · 40 hydrogen bonds · protein-nucleic
Compared structures
- 6YTF · Acinetobacter baumannii ribosome-tigecycline complex - 30S subunit head · the same entry in another collection · chain d against d, 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 D0CD03
- Every structure of UniProt D0C9P7
- Every structure of UniProt D0CG36
- Every structure of UniProt D0CCZ6
- Every structure of UniProt D0CD19
- Every structure of UniProt D0CD10
- Every structure of UniProt D0CD01
- Elsewhere: RCSB PDB 6YTF · PDBe 6YTF · UniProt D0CD03 · UniProt D0C9P7 · UniProt D0CG36 · UniProt D0CCZ6 · UniProt D0CD19 · UniProt D0CD10 · UniProt D0CD01
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