Research workbench
Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit
Analyse Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PIP
- Type
- protein + RNA
- Length
- 5,931 residues
- Chains
- 30
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosomal 23S RNA; 5S ribosomal RNA; 50S ribosomal protein L2; 50S ribosomal protein L3…
- UniProt
- Q9RXJ9, Q9RXK2, Q9RXK1, Q9RXJ0, Q9RSL3, Q9RSS7, Q9RXY1, Q9RXJ2, Q9RSK9, Q9RXJ5, Q9RSJ5, Q9RSL2, Q9RWB4, Q9RSW7, Q9RY64, Q9RXJ7, Q9RXK0, Q9RXJ1, Q9RX88, Q9RY65, Q9RRG8, Q9RXJ4, Q9RSL0, P49228, Q9RSS4, Q9RSH2, Q9RSW6, Q9RSK0
- Ligands
- LC2, LMA, MG, NA, K
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 30 distinct chains · 20% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X | Ribosomal 23S RNA | rna | 2644 | — | — |
| Y | 5S ribosomal RNA | rna | 120 | — | — |
| A | 50S ribosomal protein L2 | protein | 253 | 3% helix, 23% strand | Q9RXJ9 |
| B | 50S ribosomal protein L3 | protein | 205 | 8% helix, 38% strand | Q9RXK2 |
| C | 50S ribosomal protein L4 | protein | 194 | 27% helix, 4% strand | Q9RXK1 |
| D | 50S ribosomal protein L5 | protein | 177 | 28% helix, 18% strand | Q9RXJ0 |
| E | 50S ribosomal protein L6 | protein | 171 | 19% helix, 30% strand | Q9RSL3 |
| F | 50S ribosomal protein L11 | protein | 63 | 44% helix, 0% strand | Q9RSS7 |
| G | 50S ribosomal protein L13 | protein | 142 | 25% helix, 18% strand | Q9RXY1 |
| H | 50S ribosomal protein L14 | protein | 134 | 7% helix, 34% strand | Q9RXJ2 |
| I | 50S ribosomal protein L15 | protein | 134 | 12% helix, 9% strand | Q9RSK9 |
| J | 50S ribosomal protein L16 | protein | 136 | 19% helix, 21% strand | Q9RXJ5 |
| K | 50S ribosomal protein L17 | protein | 113 | 50% helix, 12% strand | Q9RSJ5 |
| L | 50S ribosomal protein L18 | protein | 104 | 25% helix, 9% strand | Q9RSL2 |
| M | 50S ribosomal protein L19 | protein | 108 | 9% helix, 39% strand | Q9RWB4 |
| N | 50S ribosomal protein L20 | protein | 117 | 68% helix, 0% strand | Q9RSW7 |
| O | 50S ribosomal protein L21 | protein | 94 | 4% helix, 34% strand | Q9RY64 |
| P | 50S ribosomal protein L22 | protein | 126 | 33% helix, 33% strand | Q9RXJ7 |
| Q | 50S ribosomal protein L23 | protein | 93 | 20% helix, 29% strand | Q9RXK0 |
| R | 50S ribosomal protein L24 | protein | 110 | 0% helix, 27% strand | Q9RXJ1 |
| S | 50S ribosomal protein L25 | protein | 175 | 10% helix, 34% strand | Q9RX88 |
| T | 50S ribosomal protein L27 | protein | 74 | 0% helix, 39% strand | Q9RY65 |
| U | 50S ribosomal protein L28 | protein | 72 | 13% helix, 14% strand | Q9RRG8 |
| V | 50S ribosomal protein L29 | protein | 65 | 68% helix, 0% strand | Q9RXJ4 |
| W | 50S ribosomal protein L30 | protein | 55 | 33% helix, 15% strand | Q9RSL0 |
| Z | 50S ribosomal protein L32 | protein | 57 | 18% helix, 14% strand | P49228 |
| 1 | 50S ribosomal protein L33 | protein | 53 | 0% helix, 15% strand | Q9RSS4 |
| 2 | 50S ribosomal protein L34 | protein | 46 | 46% helix, 0% strand | Q9RSH2 |
| 3 | 50S ribosomal protein L35 | protein | 59 | 14% helix, 3% strand | Q9RSW6 |
| 4 | 50S ribosomal protein L36 | protein | 37 | 8% helix, 30% strand | Q9RSK0 |
Ligands and binding sites
- LC2 · N-[(1S,2R,3E,5E,7S,9E,11E,13S,15R,19R)-7,13-dihydroxy-1,4,10,19-tetramethyl-17,18-dioxo-16-oxabicyclo[13.2.2]nonadeca-3,5,9,11-tetraen-2-yl]-2-oxopropanamide · ligand · chains X
- LMA · Lankamycin · ligand · chains X, P
- MG · Magnesium ion · metal · 73 copies · chains X, B, K, M, U, P, O, A, C, I
- NA · Sodium ion · metal · 5 copies · chains X
- K · Potassium ion · metal · 4 copies · chains X
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 | 617 | 0.86 | 0.93 | 59 | MG |
| 2 | 524 | 0.86 | 0.93 | 59 | MG |
| 3 | 1088 | 0.86 | 0.88 | 83 | MG |
| 4 | 686 | 0.86 | 0.91 | 61 | empty |
| 5 | 756 | 0.85 | 0.88 | 94 | empty |
Interfaces
58 interfaces between chains.
- X–A · 6390 Ų buried · 134 hydrogen bonds · protein-nucleic
- X–B · 5190 Ų buried · 109 hydrogen bonds · protein-nucleic
- X–N · 4381 Ų buried · 88 hydrogen bonds · protein-nucleic
- X–C · 4344 Ų buried · 86 hydrogen bonds · protein-nucleic
- X–I · 3808 Ų buried · 77 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3PIP · Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex… · the same entry in another collection · chain I against I, 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 Q9RXJ9
- Every structure of UniProt Q9RXK2
- Every structure of UniProt Q9RXK1
- Every structure of UniProt Q9RXJ0
- Every structure of UniProt Q9RSL3
- Every structure of UniProt Q9RSS7
- Every structure of UniProt Q9RXY1
- Every structure of UniProt Q9RXJ2
- Every structure of UniProt Q9RSK9
- Every structure of UniProt Q9RXJ5
- Every structure of UniProt Q9RSJ5
- Every structure of UniProt Q9RSL2
- Every structure of UniProt Q9RWB4
- Every structure of UniProt Q9RSW7
- Every structure of UniProt Q9RY64
- Every structure of UniProt Q9RXJ7
- Every structure of UniProt Q9RXK0
- Every structure of UniProt Q9RXJ1
- Every structure of UniProt Q9RX88
- Every structure of UniProt Q9RY65
- Every structure of UniProt Q9RRG8
- Every structure of UniProt Q9RXJ4
- Every structure of UniProt Q9RSL0
- Every structure of UniProt P49228
- Every structure of UniProt Q9RSS4
- Every structure of UniProt Q9RSH2
- Every structure of UniProt Q9RSW6
- Every structure of UniProt Q9RSK0
- Elsewhere: RCSB PDB 3PIP · PDBe 3PIP · UniProt Q9RXJ9 · UniProt Q9RXK2 · UniProt Q9RXK1 · UniProt Q9RXJ0 · UniProt Q9RSL3 · UniProt Q9RSS7 · UniProt Q9RXY1 · UniProt Q9RXJ2 · UniProt Q9RSK9 · UniProt Q9RXJ5 · UniProt Q9RSJ5 · UniProt Q9RSL2 · UniProt Q9RWB4 · UniProt Q9RSW7 · UniProt Q9RY64 · UniProt Q9RXJ7 · UniProt Q9RXK0 · UniProt Q9RXJ1 · UniProt Q9RX88 · UniProt Q9RY65 · UniProt Q9RRG8 · UniProt Q9RXJ4 · UniProt Q9RSL0 · UniProt P49228 · UniProt Q9RSS4 · UniProt Q9RSH2 · UniProt Q9RSW6 · UniProt Q9RSK0
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