MolNFT v1 · #164168 · protein + RNA
Pseudomonas aeruginosa 50S ribosome from a clinical isolate with a mutation in UL6
6SPB · 23S ribosomal RNA: “Pseudomonas aeruginosa 50S ribosome from a clinical isolate with a mutation in UL6”. Electron microscopy, 20 pockets (best druggability 0.88). MolNFT v1 #164168 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6SPB
- Type
- protein + RNA
- Length
- 6,385 residues
- Chains
- 32
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 23S ribosomal RNA; 5S rRNA; 50S ribosomal protein L2; 50S ribosomal protein L3; 50S…
- UniProt
- A0A241XHA2, A0A072ZBZ2, A0A241XH26, A0A072ZMU2, A0A2V3F3S9, A0A072ZKF0, A0A2V3GYK0, A0A071L356, E2RXT6, A0A2V3D5Z8, A0A069QEB6, A0A072ZCA1, E2RXU0, A0A263PZC6, A0A069QEE3, A0A072ZDZ0, A0A1C7BCP0, E2RXT1, E2RXT7, A0A072ZBM5, A0A071LFT4, A0A072ZIQ9, W6V2V8, E2RXU1, A0A072ZJG4, A0A069QB25, A0A140SG33, A0A087L9L7, A0A069QC44, E2RXU2
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 32 distinct chains · 21% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 23S ribosomal RNA | rna | 2885 | — | — |
| B | 5S rRNA | rna | 117 | — | — |
| C | 50S ribosomal protein L2 | protein | 271 | 5% helix, 27% strand | A0A241XHA2 |
| D | 50S ribosomal protein L3 | protein | 207 | 12% helix, 36% strand | A0A072ZBZ2 |
| E | 50S ribosomal protein L4 | protein | 199 | 30% helix, 10% strand | A0A241XH26 |
| F | 50S ribosomal protein L5 | protein | 174 | 18% helix, 1% strand | A0A072ZMU2 |
| G | 50S ribosomal protein L6 | protein | 169 | 20% helix, 26% strand | A0A2V3F3S9 |
| H | 50S ribosomal protein L9 | protein | 78 | 37% helix, 10% strand | A0A072ZKF0 |
| I | 50S ribosomal protein L11 | protein | 140 | 5% helix, 0% strand | A0A2V3GYK0 |
| J | 50S ribosomal protein L13 | protein | 141 | 28% helix, 16% strand | A0A071L356 |
| K | 50S ribosomal protein L14 | protein | 120 | 8% helix, 37% strand | E2RXT6 |
| L | 50S ribosomal protein L15 | protein | 143 | 15% helix, 13% strand | A0A2V3D5Z8 |
| M | 50S ribosomal protein L16 | protein | 135 | 19% helix, 27% strand | A0A069QEB6 |
| N | 50S ribosomal protein L17 | protein | 118 | 42% helix, 19% strand | A0A072ZCA1 |
| O | 50S ribosomal protein L18 | protein | 115 | 38% helix, 18% strand | E2RXU0 |
| P | 50S ribosomal protein L19 | protein | 113 | 10% helix, 41% strand | A0A263PZC6 |
| Q | 50S ribosomal protein L20 | protein | 117 | 76% helix, 0% strand | A0A069QEE3 |
| R | 50S ribosomal protein L21 | protein | 102 | 0% helix, 67% strand | A0A072ZDZ0 |
| S | 50S ribosomal protein L22 | protein | 109 | 39% helix, 35% strand | A0A1C7BCP0 |
| T | 50S ribosomal protein L23 | protein | 92 | 21% helix, 38% strand | E2RXT1 |
| U | 50S ribosomal protein L24 | protein | 103 | 3% helix, 38% strand | E2RXT7 |
| V | 50S ribosomal protein L25 | protein | 188 | 10% helix, 28% strand | A0A072ZBM5 |
| W | 50S ribosomal protein L27 | protein | 76 | 4% helix, 36% strand | A0A071LFT4 |
| X | 50S ribosomal protein L28 | protein | 77 | 31% helix, 29% strand | A0A072ZIQ9 |
| Y | 50S ribosomal protein L29 | protein | 60 | 75% helix, 0% strand | W6V2V8 |
| Z | 50S ribosomal protein L30 | protein | 57 | 37% helix, 25% strand | E2RXU1 |
| 1 | 50S ribosomal protein L31 | protein | 31 | 0% helix, 0% strand | A0A072ZJG4 |
| 2 | 50S ribosomal protein L32 | protein | 53 | 13% helix, 17% strand | A0A069QB25 |
| 3 | 50S ribosomal protein L33 | protein | 50 | 0% helix, 44% strand | A0A140SG33 |
| 4 | 50S ribosomal protein L34 | protein | 44 | 57% helix, 0% strand | A0A087L9L7 |
| 5 | 50S ribosomal protein L35 | protein | 63 | 30% helix, 13% strand | A0A069QC44 |
| 6 | 50S ribosomal protein L36 | protein | 38 | 8% helix, 34% strand | E2RXU2 |
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 | 945 | 0.88 | 0.91 | 105 | empty |
| 2 | 1073 | 0.88 | 0.90 | 89 | empty |
| 3 | 1118 | 0.87 | 0.89 | 107 | empty |
| 4 | 1090 | 0.87 | 0.88 | 133 | empty |
| 5 | 760 | 0.87 | 0.91 | 72 | empty |
Interfaces
61 interfaces between chains.
- A–C · 7236 Ų buried · 186 hydrogen bonds · protein-nucleic
- A–I · 7043 Ų buried · 180 hydrogen bonds · protein-nucleic
- A–D · 5066 Ų buried · 117 hydrogen bonds · protein-nucleic
- A–L · 4570 Ų buried · 103 hydrogen bonds · protein-nucleic
- A–E · 4272 Ų buried · 90 hydrogen bonds · protein-nucleic
Compared structures
- 6SPB · Pseudomonas aeruginosa 50s ribosome from a clinical isolate with a mutation in uL6 · the same entry in another collection · chain B against B, 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 A0A241XHA2
- Every structure of UniProt A0A072ZBZ2
- Every structure of UniProt A0A241XH26
- Every structure of UniProt A0A072ZMU2
- Every structure of UniProt A0A2V3F3S9
- Every structure of UniProt A0A072ZKF0
- Every structure of UniProt A0A2V3GYK0
- Every structure of UniProt A0A071L356
- Every structure of UniProt E2RXT6
- Every structure of UniProt A0A2V3D5Z8
- Every structure of UniProt A0A069QEB6
- Every structure of UniProt A0A072ZCA1
- Every structure of UniProt E2RXU0
- Every structure of UniProt A0A263PZC6
- Every structure of UniProt A0A069QEE3
- Every structure of UniProt A0A072ZDZ0
- Every structure of UniProt A0A1C7BCP0
- Every structure of UniProt E2RXT1
- Every structure of UniProt E2RXT7
- Every structure of UniProt A0A072ZBM5
- Every structure of UniProt A0A071LFT4
- Every structure of UniProt A0A072ZIQ9
- Every structure of UniProt W6V2V8
- Every structure of UniProt E2RXU1
- Every structure of UniProt A0A072ZJG4
- Every structure of UniProt A0A069QB25
- Every structure of UniProt A0A140SG33
- Every structure of UniProt A0A087L9L7
- Every structure of UniProt A0A069QC44
- Every structure of UniProt E2RXU2
- Elsewhere: RCSB PDB 6SPB · PDBe 6SPB · UniProt A0A241XHA2 · UniProt A0A072ZBZ2 · UniProt A0A241XH26 · UniProt A0A072ZMU2 · UniProt A0A2V3F3S9 · UniProt A0A072ZKF0 · UniProt A0A2V3GYK0 · UniProt A0A071L356 · UniProt E2RXT6 · UniProt A0A2V3D5Z8 · UniProt A0A069QEB6 · UniProt A0A072ZCA1 · UniProt E2RXU0 · UniProt A0A263PZC6 · UniProt A0A069QEE3 · UniProt A0A072ZDZ0 · UniProt A0A1C7BCP0 · UniProt E2RXT1 · UniProt E2RXT7 · UniProt A0A072ZBM5 · UniProt A0A071LFT4 · UniProt A0A072ZIQ9 · UniProt W6V2V8 · UniProt E2RXU1 · UniProt A0A072ZJG4 · UniProt A0A069QB25 · UniProt A0A140SG33 · UniProt A0A087L9L7 · UniProt A0A069QC44 · UniProt E2RXU2
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