Research workbench
Structure of an archaeal ABCE1-bound ribosomal post-splitting complex
Analyse Structure of an archaeal ABCE1-bound ribosomal post-splitting complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TMF
- Type
- protein + RNA
- Length
- 5,657 residues
- Chains
- 30
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 16S ribosomal RNA; 30S ribosomal protein S2; 30S ribosomal protein S3; 30S ribosomal…
- UniProt
- A0A218NZR2, A0A218NZU7, A0A218P0R0, A0A218NZV3, A0A218NZX1, A0A218P4N5, A0A218P2W6, A0A218P4K4, A0A218NZT7, A0A218P4F6, A0A218NZS6, A0A218P3Q8, A0A218NZU0, A0A218P4I2, A0A218NZT2, A0A218NZW1, A0A218P0Q1, A0A218NZX3, A0A218P2C1, A0A218P4M9, A0A218P4W7, A0A218P055, A0A218P0B9, A0A218NZS1, A0A218P0A5, A0A218P147, A0A218P167, A0A218P2S9, A0A0E3MFT8
- Ligands
- SF4, ANP, MG, ZN
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 30 distinct chains · 31% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 16S ribosomal RNA | rna | 1485 | — | — |
| B | 30S ribosomal protein S2 | protein | 195 | 37% helix, 13% strand | A0A218NZR2 |
| C | 30S ribosomal protein S3 | protein | 193 | 40% helix, 28% strand | A0A218NZU7 |
| D | 30S ribosomal protein S3AE | protein | 184 | 26% helix, 33% strand | A0A218P0R0 |
| E | 30S ribosomal protein S4 | protein | 178 | 51% helix, 6% strand | A0A218NZV3 |
| F | 30S ribosomal protein S4E | protein | 241 | 13% helix, 36% strand | A0A218NZX1 |
| G | 30S ribosomal protein S5 | protein | 220 | 34% helix, 28% strand | A0A218P4N5 |
| H | 30S ribosomal protein S6E | protein | 125 | 8% helix, 36% strand | A0A218P2W6 |
| I | 30S ribosomal protein S7 | protein | 214 | 43% helix, 11% strand | A0A218P4K4 |
| J | 30S ribosomal protein S8 | protein | 129 | 32% helix, 34% strand | A0A218NZT7 |
| K | 30S ribosomal protein S8E | protein | 126 | 10% helix, 40% strand | A0A218P4F6 |
| L | 30S ribosomal protein S9 | protein | 132 | 41% helix, 20% strand | A0A218NZS6 |
| M | 30S ribosomal protein S10 | protein | 102 | 25% helix, 45% strand | A0A218P3Q8 |
| N | 30S ribosomal protein S11 | protein | 133 | 27% helix, 26% strand | A0A218NZU0 |
| O | 30S ribosomal protein S12 | protein | 144 | 24% helix, 27% strand | A0A218P4I2 |
| P | 30S ribosomal protein S13 | protein | 136 | 43% helix, 6% strand | A0A218NZT2 |
| Q | 30S ribosomal protein S14 type Z | protein | 56 | 20% helix, 9% strand | A0A218NZW1 |
| R | 30S ribosomal protein S15 | protein | 151 | 58% helix, 0% strand | A0A218P0Q1 |
| S | 30S ribosomal protein S17 | protein | 111 | 0% helix, 39% strand | A0A218NZX3 |
| T | 30S ribosomal protein S17E | protein | 64 | 72% helix, 0% strand | A0A218P2C1 |
| U | 30S ribosomal protein S19P | protein | 115 | 37% helix, 13% strand | A0A218P4M9 |
| V | 30S ribosomal protein S19E | protein | 149 | 47% helix, 13% strand | A0A218P4W7 |
| W | RNA-binding protein | protein | 56 | 9% helix, 14% strand | A0A218P055 |
| X | 30S ribosomal protein S24E | protein | 97 | 25% helix, 36% strand | A0A218P0B9 |
| Y | 30S ribosomal protein S27E | protein | 63 | 0% helix, 32% strand | A0A218NZS1 |
| Z | 30S ribosomal protein S27AE | protein | 50 | 0% helix, 12% strand | A0A218P0A5 |
| a | 30S ribosomal protein S28E | protein | 66 | 0% helix, 42% strand | A0A218P147 |
| b | 50S ribosomal protein L7AE | protein | 123 | 44% helix, 12% strand | A0A218P167 |
| c | Lsu ribosomal protein L41E | protein | 37 | 65% helix, 0% strand | A0A218P2S9 |
| d | ATPase | protein | 582 | 32% helix, 17% strand | A0A0E3MFT8 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains d
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains d
- MG · Magnesium ion · metal · 29 copies · chains A, T, V, G, d
- ZN · Zinc ion · metal · 4 copies · chains Q, W, Y
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 | 684 | 0.88 | 0.93 | 88 | MG |
| 2 | 809 | 0.87 | 0.90 | 93 | empty |
| 3 | 1063 | 0.85 | 0.87 | 85 | empty |
| 4 | 637 | 0.85 | 0.90 | 71 | empty |
| 5 | 769 | 0.84 | 0.88 | 82 | empty |
Interfaces
66 interfaces between chains.
- A–F · 3993 Ų buried · 81 hydrogen bonds · protein-nucleic
- A–O · 3571 Ų buried · 84 hydrogen bonds · protein-nucleic
- A–K · 3372 Ų buried · 75 hydrogen bonds · protein-nucleic
- A–E · 3287 Ų buried · 78 hydrogen bonds · protein-nucleic
- A–R · 3232 Ų buried · 66 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6TMF · Structure of an archaeal ABCE1-bound ribosomal post-splitting complex · 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 A0A218NZR2
- Every structure of UniProt A0A218NZU7
- Every structure of UniProt A0A218P0R0
- Every structure of UniProt A0A218NZV3
- Every structure of UniProt A0A218NZX1
- Every structure of UniProt A0A218P4N5
- Every structure of UniProt A0A218P2W6
- Every structure of UniProt A0A218P4K4
- Every structure of UniProt A0A218NZT7
- Every structure of UniProt A0A218P4F6
- Every structure of UniProt A0A218NZS6
- Every structure of UniProt A0A218P3Q8
- Every structure of UniProt A0A218NZU0
- Every structure of UniProt A0A218P4I2
- Every structure of UniProt A0A218NZT2
- Every structure of UniProt A0A218NZW1
- Every structure of UniProt A0A218P0Q1
- Every structure of UniProt A0A218NZX3
- Every structure of UniProt A0A218P2C1
- Every structure of UniProt A0A218P4M9
- Every structure of UniProt A0A218P4W7
- Every structure of UniProt A0A218P055
- Every structure of UniProt A0A218P0B9
- Every structure of UniProt A0A218NZS1
- Every structure of UniProt A0A218P0A5
- Every structure of UniProt A0A218P147
- Every structure of UniProt A0A218P167
- Every structure of UniProt A0A218P2S9
- Every structure of UniProt A0A0E3MFT8
- Elsewhere: RCSB PDB 6TMF · PDBe 6TMF · UniProt A0A218NZR2 · UniProt A0A218NZU7 · UniProt A0A218P0R0 · UniProt A0A218NZV3 · UniProt A0A218NZX1 · UniProt A0A218P4N5 · UniProt A0A218P2W6 · UniProt A0A218P4K4 · UniProt A0A218NZT7 · UniProt A0A218P4F6 · UniProt A0A218NZS6 · UniProt A0A218P3Q8 · UniProt A0A218NZU0 · UniProt A0A218P4I2 · UniProt A0A218NZT2 · UniProt A0A218NZW1 · UniProt A0A218P0Q1 · UniProt A0A218NZX3 · UniProt A0A218P2C1 · UniProt A0A218P4M9 · UniProt A0A218P4W7 · UniProt A0A218P055 · UniProt A0A218P0B9 · UniProt A0A218NZS1 · UniProt A0A218P0A5 · UniProt A0A218P147 · UniProt A0A218P167 · UniProt A0A218P2S9 · UniProt A0A0E3MFT8
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