MolNFT v1 · #188479 · protein + RNA
50S ribosomal subunit from staphylococcus aureus (strain ATCC43300)
7TTU · 50S ribosomal protein L19: “50S ribosomal subunit from staphylococcus aureus (strain ATCC43300)”. Electron microscopy, 20 pockets (best druggability 0.89). MolNFT v1 #188479 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7TTU
- Type
- protein + RNA
- Length
- 5,456 residues
- Chains
- 27
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 50S ribosomal protein L19; 50S ribosomal protein L2; 50S ribosomal protein L20; 50S…
- UniProt
- A0A077UVB6, A0A077W1J0, A0A077VMP6, D7URR3, A0A0D1H5C2, W8TUB4, W8TRD5, A0A133Q8Z9, A0A0D1H0B5, A0A077URJ8, A0A7R6P2U0, A0A0D1GR95, W8UVN7, A0A077UWR7, A0A077UXT4, Q2YZB6, A0A0D1H088, A0A077UGV8, A0A166DK89, W8TUE6, A0A077UUA0, A0A077UGA7, A0A077V4G0, A0A077UG91, W8TRE0
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 27 distinct chains · 22% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 50S ribosomal protein L19 | protein | 113 | 12% helix, 38% strand | A0A077UVB6 |
| B | 50S ribosomal protein L2 | protein | 273 | 8% helix, 27% strand | A0A077W1J0 |
| C | 50S ribosomal protein L20 | protein | 116 | 78% helix, 0% strand | A0A077VMP6 |
| D | 50S ribosomal protein L21 | protein | 100 | 0% helix, 54% strand | D7URR3 |
| E | 50S ribosomal protein L22 | protein | 111 | 33% helix, 35% strand | A0A0D1H5C2 |
| F | 50S ribosomal protein L23 | protein | 87 | 20% helix, 38% strand | W8TUB4 |
| G | 50S ribosomal protein L24 | protein | 90 | 3% helix, 43% strand | W8TRD5 |
| H | 50S ribosomal protein L25 | protein | 93 | 23% helix, 51% strand | A0A133Q8Z9 |
| I | 50S ribosomal protein L27 | protein | 78 | 0% helix, 36% strand | A0A0D1H0B5 |
| J | 50S ribosomal protein L28 | protein | 59 | 7% helix, 37% strand | A0A077URJ8 |
| K | 50S ribosomal protein L29 | protein | 61 | 70% helix, 0% strand | A0A7R6P2U0 |
| L | 50S ribosomal protein L3 | protein | 215 | 9% helix, 36% strand | A0A0D1GR95 |
| M | 50S ribosomal protein L30 | protein | 56 | 32% helix, 21% strand | W8UVN7 |
| N | 50S ribosomal protein L32 | protein | 50 | 14% helix, 12% strand | A0A077UWR7 |
| O | 50S ribosomal protein L33 | protein | 47 | 0% helix, 53% strand | A0A077UXT4 |
| P | 50S ribosomal protein L34 | protein | 44 | 57% helix, 0% strand | Q2YZB6 |
| Q | 50S ribosomal protein L35 | protein | 64 | 27% helix, 11% strand | A0A0D1H088 |
| R | 50S ribosomal protein L36 | protein | 37 | 8% helix, 32% strand | A0A077UGV8 |
| S | 50S ribosomal protein L4 | protein | 192 | 33% helix, 11% strand | A0A166DK89 |
| V | 50S ribosomal protein L13 | protein | 143 | 29% helix, 19% strand | W8TUE6 |
| W | 50S ribosomal protein L14 | protein | 121 | 7% helix, 36% strand | A0A077UUA0 |
| X | 50S ribosomal protein L15 | protein | 144 | 17% helix, 12% strand | A0A077UGA7 |
| Y | 50S ribosomal protein L16 | protein | 136 | 18% helix, 28% strand | A0A077V4G0 |
| Z | 50S ribosomal protein L17 | protein | 121 | 42% helix, 20% strand | A0A077UG91 |
| a | 50S ribosomal protein L18 | protein | 110 | 32% helix, 24% strand | W8TRE0 |
| 1 | 23S rRNA | rna | 2684 | — | — |
| 2 | 5S rRNA | rna | 111 | — | — |
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 | 1014 | 0.89 | 0.91 | 87 | empty |
| 2 | 923 | 0.88 | 0.91 | 91 | empty |
| 3 | 1188 | 0.87 | 0.89 | 100 | empty |
| 4 | 852 | 0.87 | 0.90 | 82 | empty |
| 5 | 782 | 0.87 | 0.91 | 87 | empty |
Interfaces
51 interfaces between chains.
- B–1 · 6773 Ų buried · 116 hydrogen bonds · protein-nucleic
- L–1 · 5054 Ų buried · 73 hydrogen bonds · protein-nucleic
- X–1 · 4424 Ų buried · 77 hydrogen bonds · protein-nucleic
- S–1 · 4271 Ų buried · 61 hydrogen bonds · protein-nucleic
- C–1 · 3971 Ų buried · 75 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7TTU · 50S ribosomal subunit from Staphylococcus aureus (Strain ATCC43300) · 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 A0A077UVB6
- Every structure of UniProt A0A077W1J0
- Every structure of UniProt A0A077VMP6
- Every structure of UniProt D7URR3
- Every structure of UniProt A0A0D1H5C2
- Every structure of UniProt W8TUB4
- Every structure of UniProt W8TRD5
- Every structure of UniProt A0A133Q8Z9
- Every structure of UniProt A0A0D1H0B5
- Every structure of UniProt A0A077URJ8
- Every structure of UniProt A0A7R6P2U0
- Every structure of UniProt A0A0D1GR95
- Every structure of UniProt W8UVN7
- Every structure of UniProt A0A077UWR7
- Every structure of UniProt A0A077UXT4
- Every structure of UniProt Q2YZB6
- Every structure of UniProt A0A0D1H088
- Every structure of UniProt A0A077UGV8
- Every structure of UniProt A0A166DK89
- Every structure of UniProt W8TUE6
- Every structure of UniProt A0A077UUA0
- Every structure of UniProt A0A077UGA7
- Every structure of UniProt A0A077V4G0
- Every structure of UniProt A0A077UG91
- Every structure of UniProt W8TRE0
- Elsewhere: RCSB PDB 7TTU · PDBe 7TTU · UniProt A0A077UVB6 · UniProt A0A077W1J0 · UniProt A0A077VMP6 · UniProt D7URR3 · UniProt A0A0D1H5C2 · UniProt W8TUB4 · UniProt W8TRD5 · UniProt A0A133Q8Z9 · UniProt A0A0D1H0B5 · UniProt A0A077URJ8 · UniProt A0A7R6P2U0 · UniProt A0A0D1GR95 · UniProt W8UVN7 · UniProt A0A077UWR7 · UniProt A0A077UXT4 · UniProt Q2YZB6 · UniProt A0A0D1H088 · UniProt A0A077UGV8 · UniProt A0A166DK89 · UniProt W8TUE6 · UniProt A0A077UUA0 · UniProt A0A077UGA7 · UniProt A0A077V4G0 · UniProt A0A077UG91 · UniProt W8TRE0
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