Research workbench
M. smegmatis P/P state 30S ribosomal subunit
Analyse M. smegmatis P/P state 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
- 5ZEU
- Type
- protein + RNA
- Length
- 3,989 residues
- Chains
- 22
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 16S rRNA; 30S ribosomal protein S3; 30S ribosomal protein S5; 30S ribosomal protein S7…
- UniProt
- A0QSD7, A0QSG6, A0QS97, A0QSG3, A0QSP9, A0QSD0, A0QSL6, A0QS96, A0QVQ3, A0QSE0, A0R7F7, A0QSD5, A0R102, A0QSG2, A0QVB8, A0QSL7, A0A0D6J3X3, A0QSL5, A0QV37, A0QR10
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 22 distinct chains · 37% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| a | 16S rRNA | rna | 1506 | — | — |
| c | 30S ribosomal protein S3 | protein | 210 | 27% helix, 23% strand | A0QSD7 |
| e | 30S ribosomal protein S5 | protein | 198 | 32% helix, 30% strand | A0QSG6 |
| g | 30S ribosomal protein S7 | protein | 156 | 58% helix, 5% strand | A0QS97 |
| h | 30S ribosomal protein S8 | protein | 130 | 27% helix, 25% strand | A0QSG3 |
| i | 30S ribosomal protein S9 | protein | 126 | 33% helix, 18% strand | A0QSP9 |
| j | 30S ribosomal protein S10 | protein | 97 | 28% helix, 41% strand | A0QSD0 |
| k | 30S ribosomal protein S11 | protein | 117 | 29% helix, 25% strand | A0QSL6 |
| l | 30S ribosomal protein S12 | protein | 122 | 4% helix, 25% strand | A0QS96 |
| o | 30S ribosomal protein S15 | protein | 87 | 72% helix, 0% strand | A0QVQ3 |
| q | 30S ribosomal protein S17 | protein | 92 | 0% helix, 35% strand | A0QSE0 |
| r | 30S ribosomal protein S18 2 | protein | 64 | 39% helix, 3% strand | A0R7F7 |
| s | 30S ribosomal protein S19 | protein | 78 | 28% helix, 17% strand | A0QSD5 |
| t | 30S ribosomal protein S20 | protein | 84 | 82% helix, 0% strand | A0R102 |
| v | P-trnafmet | rna | 77 | — | — |
| n | 30S ribosomal protein S14 type Z | protein | 60 | 30% helix, 8% strand | A0QSG2 |
| b | 30S ribosomal protein S2 | protein | 228 | 46% helix, 12% strand | A0QVB8 |
| d | 30S ribosomal protein S4 | protein | 200 | 44% helix, 7% strand | A0QSL7 |
| f | 30S ribosomal protein S6 | protein | 96 | 30% helix, 33% strand | A0A0D6J3X3 |
| m | 30S ribosomal protein S13 | protein | 116 | 49% helix, 0% strand | A0QSL5 |
| p | 30S ribosomal protein S16 | protein | 113 | 33% helix, 23% strand | A0QV37 |
| u | Conserved domain protein | protein | 32 | 88% helix, 0% strand | A0QR10 |
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 | 990 | 0.85 | 0.88 | 84 | empty |
| 2 | 675 | 0.85 | 0.90 | 73 | empty |
| 3 | 1091 | 0.85 | 0.87 | 87 | empty |
| 4 | 1063 | 0.85 | 0.86 | 95 | empty |
| 5 | 924 | 0.83 | 0.86 | 51 | empty |
Interfaces
42 interfaces between chains.
- a–l · 3061 Ų buried · 68 hydrogen bonds · protein-nucleic
- a–i · 3052 Ų buried · 96 hydrogen bonds · protein-nucleic
- a–d · 3005 Ų buried · 73 hydrogen bonds · protein-nucleic
- a–q · 2706 Ų buried · 52 hydrogen bonds · protein-nucleic
- a–t · 2446 Ų buried · 56 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5ZEU · M. smegmatis P/P state 30S ribosomal subunit · the same entry in another collection · chain o against o, 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 A0QSD7
- Every structure of UniProt A0QSG6
- Every structure of UniProt A0QS97
- Every structure of UniProt A0QSG3
- Every structure of UniProt A0QSP9
- Every structure of UniProt A0QSD0
- Every structure of UniProt A0QSL6
- Every structure of UniProt A0QS96
- Every structure of UniProt A0QVQ3
- Every structure of UniProt A0QSE0
- Every structure of UniProt A0R7F7
- Every structure of UniProt A0QSD5
- Every structure of UniProt A0R102
- Every structure of UniProt A0QSG2
- Every structure of UniProt A0QVB8
- Every structure of UniProt A0QSL7
- Every structure of UniProt A0A0D6J3X3
- Every structure of UniProt A0QSL5
- Every structure of UniProt A0QV37
- Every structure of UniProt A0QR10
- Elsewhere: RCSB PDB 5ZEU · PDBe 5ZEU · UniProt A0QSD7 · UniProt A0QSG6 · UniProt A0QS97 · UniProt A0QSG3 · UniProt A0QSP9 · UniProt A0QSD0 · UniProt A0QSL6 · UniProt A0QS96 · UniProt A0QVQ3 · UniProt A0QSE0 · UniProt A0R7F7 · UniProt A0QSD5 · UniProt A0R102 · UniProt A0QSG2 · UniProt A0QVB8 · UniProt A0QSL7 · UniProt A0A0D6J3X3 · UniProt A0QSL5 · UniProt A0QV37 · UniProt A0QR10
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