Research workbench
Mtb 70SIC in complex with MtbEttA at Pre_R1 state
Analyse Mtb 70SIC in complex with MtbEttA at Pre_R1 state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MSH
- Type
- protein + RNA
- Length
- 10,982 residues
- Chains
- 55
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.23
- Source
- Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv); Mycobacterium…
- Molecule
- 50S ribosomal protein L32; 50S ribosomal protein L33 2; 50S ribosomal protein L34; 50S…
- EC
- 3.6.1.-
- UniProt
- P9WH99, P9WH95, P9WH93, P9WH91, P9WH89, P9WHA1, A0A3E0UTA6, P9WHC7, P9WHA5, P9WH87, P9WH85, P9WH83, P9WH81, P9WH79, A0A0T9D5H2, A0A045HTP7, P9WHD7, P9WHD5, P9WHD3, P9WHD1, P9WHC9, P9WHC5, P9WHC3, P9WHC1, P9WHB9, P9WHB7, P9WHB5, P9WHB3, A0A045IDB8, P9WHA7, P9WHA3, P9WH37, P9WH35, P9WH33, P9WH31, P9WH29, P9WH27, P9WH25, P9WH67, P9WH65, P9WH63, P9WH61, P9WH57, P9WH55, P9WH53, P9WH51, P9WH49, P9WH45, P9WH41, P9WQK3
- Ligands
- ANP, MG, ZN
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · resolution 3.23 · 55 distinct chains · 23% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 0 | 50S ribosomal protein L32 | protein | 54 | 26% helix, 11% strand | P9WH99 |
| 1 | 50S ribosomal protein L33 2 | protein | 48 | 0% helix, 44% strand | P9WH95 |
| 2 | 50S ribosomal protein L34 | protein | 44 | 36% helix, 0% strand | P9WH93 |
| 3 | 50S ribosomal protein L35 | protein | 62 | 11% helix, 11% strand | P9WH91 |
| 4 | 50S ribosomal protein L36 | protein | 37 | 8% helix, 35% strand | P9WH89 |
| 6 | 50S ribosomal protein L31 | protein | 47 | 0% helix, 30% strand | P9WHA1 |
| 7 | 50S ribosomal protein L37 | protein | 8 | 0% helix, 0% strand | A0A3E0UTA6 |
| 8 | 50S ribosomal protein L1 | protein | 230 | 22% helix, 12% strand | P9WHC7 |
| A | 23S rRNA | rna | 3118 | — | — |
| B | 5S rRNA | rna | 115 | — | — |
| C | 50S ribosomal protein L2 | protein | 272 | 6% helix, 26% strand | P9WHA5 |
| D | 50S ribosomal protein L3 | protein | 213 | 5% helix, 33% strand | P9WH87 |
| E | 50S ribosomal protein L4 | protein | 207 | 32% helix, 11% strand | P9WH85 |
| F | 50S ribosomal protein L5 | protein | 178 | 30% helix, 18% strand | P9WH83 |
| G | 50S ribosomal protein L6 | protein | 174 | 20% helix, 21% strand | P9WH81 |
| H | 50S ribosomal protein L9 | protein | 47 | 11% helix, 26% strand | P9WH79 |
| J | 50S ribosomal protein L13 | protein | 146 | 26% helix, 17% strand | A0A0T9D5H2 |
| K | 50S ribosomal protein L14 | protein | 122 | 9% helix, 33% strand | A0A045HTP7 |
| L | 50S ribosomal protein L15 | protein | 144 | 14% helix, 8% strand | P9WHD7 |
| M | 50S ribosomal protein L16 | protein | 134 | 20% helix, 25% strand | P9WHD5 |
| N | 50S ribosomal protein L17 | protein | 116 | 44% helix, 19% strand | P9WHD3 |
| O | 50S ribosomal protein L18 | protein | 119 | 31% helix, 14% strand | P9WHD1 |
| P | 50S ribosomal protein L19 | protein | 112 | 0% helix, 38% strand | P9WHC9 |
| Q | 50S ribosomal protein L20 | protein | 124 | 65% helix, 0% strand | P9WHC5 |
| R | 50S ribosomal protein L21 | protein | 100 | 0% helix, 47% strand | P9WHC3 |
| S | 50S ribosomal protein L22 | protein | 113 | 23% helix, 33% strand | P9WHC1 |
| T | 50S ribosomal protein L23 | protein | 95 | 15% helix, 37% strand | P9WHB9 |
| U | 50S ribosomal protein L24 | protein | 90 | 3% helix, 42% strand | P9WHB7 |
| V | 50S ribosomal protein L25 | protein | 177 | 9% helix, 42% strand | P9WHB5 |
| W | 50S ribosomal protein L27 | protein | 72 | 0% helix, 32% strand | P9WHB3 |
| X | 50S ribosomal protein L28 | protein | 62 | 6% helix, 32% strand | A0A045IDB8 |
| Y | 50S ribosomal protein L29 | protein | 68 | 54% helix, 0% strand | P9WHA7 |
| Z | 50S ribosomal protein L30 | protein | 59 | 24% helix, 25% strand | P9WHA3 |
| a | 16S rRNA | rna | 1519 | — | — |
| c | 30S ribosomal protein S3 | protein | 207 | 25% helix, 27% strand | P9WH37 |
| d | 30S ribosomal protein S4 | protein | 200 | 30% helix, 7% strand | P9WH35 |
| e | 30S ribosomal protein S5 | protein | 169 | 28% helix, 26% strand | P9WH33 |
| f | 30S ribosomal protein S6 | protein | 95 | 21% helix, 32% strand | P9WH31 |
| g | 30S ribosomal protein S7 | protein | 155 | 50% helix, 4% strand | P9WH29 |
| h | 30S ribosomal protein S8 | protein | 131 | 24% helix, 27% strand | P9WH27 |
| i | 30S ribosomal protein S9 | protein | 127 | 35% helix, 11% strand | P9WH25 |
| j | 30S ribosomal protein S10 | protein | 99 | 11% helix, 28% strand | P9WH67 |
| k | 30S ribosomal protein S11 | protein | 117 | 21% helix, 20% strand | P9WH65 |
| l | 30S ribosomal protein S12 | protein | 122 | 4% helix, 21% strand | P9WH63 |
| m | 30S ribosomal protein S13 | protein | 116 | 34% helix, 0% strand | P9WH61 |
| n | 30S ribosomal protein S14 type Z | protein | 60 | 35% helix, 5% strand | P9WH57 |
| o | 30S ribosomal protein S15 | protein | 87 | 66% helix, 0% strand | P9WH55 |
| p | 30S ribosomal protein S16 | protein | 113 | 25% helix, 22% strand | P9WH53 |
| q | 30S ribosomal protein S17 | protein | 95 | 0% helix, 46% strand | P9WH51 |
| r | 30S ribosomal protein S18 1 | protein | 64 | 25% helix, 3% strand | P9WH49 |
| s | 30S ribosomal protein S19 | protein | 83 | 13% helix, 16% strand | P9WH45 |
| t | 30S ribosomal protein S20 | protein | 85 | 79% helix, 0% strand | P9WH41 |
| x | Energy-dependent translational throttle protein EttA (EC 3.6.1.-) | protein | 550 | 23% helix, 14% strand | P9WQK3 |
| y | initiator tRNA (Met) | rna | 75 | — | — |
| z | mRNA | rna | 6 | — | — |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains x
- MG · Magnesium ion · metal · 420 copies · chains 3, A, C, 0, Q, E, D, N, T, 2, J, M, P, W, 1, R, B, H, X, L, a, o, n, e, d, x, t, z, r, y
- ZN · Zinc ion · metal · 6 copies · chains 1, 4, 6, X, n, r
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 | 1145 | 0.88 | 0.90 | 117 | MG |
| 2 | 832 | 0.87 | 0.90 | 96 | MG |
| 3 | 826 | 0.86 | 0.90 | 73 | MG |
| 4 | 837 | 0.86 | 0.90 | 78 | MG |
| 5 | 685 | 0.86 | 0.91 | 55 | MG |
Interfaces
120 interfaces between chains.
- A–C · 7161 Ų buried · 164 hydrogen bonds · protein-nucleic
- A–D · 4902 Ų buried · 85 hydrogen bonds · protein-nucleic
- A–L · 4546 Ų buried · 104 hydrogen bonds · protein-nucleic
- A–E · 4469 Ų buried · 90 hydrogen bonds · protein-nucleic
- A–Q · 4468 Ų buried · 108 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 9 modified (nucleotide modification).
Compared structures
- P9WHA5 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L2 (P9WHA5) · a predicted model of the same protein · chain C against A, TM-score 0.99
- P9WHD3 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L17 (P9WHD3) · a predicted model of the same protein · chain N against A, TM-score 0.99
- P9WHC5 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L20 (P9WHC5) · a predicted model of the same protein · chain Q against A, TM-score 0.99
- P9WHC1 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L22 (P9WHC1) · a predicted model of the same protein · chain S against A, TM-score 0.99
- P9WH27 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S8 (P9WH27) · a predicted model of the same protein · chain h against A, TM-score 0.99
- P9WH33 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S5 (P9WH33) · a predicted model of the same protein · chain e against A, TM-score 0.98
- P9WHD5 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L16 (P9WHD5) · a predicted model of the same protein · chain M against A, TM-score 0.98
- P9WH85 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L4 (P9WH85) · a predicted model of the same protein · chain E against A, TM-score 0.98
- P9WHD1 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L18 (P9WHD1) · a predicted model of the same protein · chain O against A, TM-score 0.98
- P9WH87 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L3 (P9WH87) · a predicted model of the same protein · chain D against A, TM-score 0.98
- P9WH37 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S3 (P9WH37) · a predicted model of the same protein · chain c against A, TM-score 0.98
- P9WH35 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S4 (P9WH35) · a predicted model of the same protein · chain d against A, TM-score 0.98
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 P9WH99
- Every structure of UniProt P9WH95
- Every structure of UniProt P9WH93
- Every structure of UniProt P9WH91
- Every structure of UniProt P9WH89
- Every structure of UniProt P9WHA1
- Every structure of UniProt A0A3E0UTA6
- Every structure of UniProt P9WHC7
- Every structure of UniProt P9WHA5
- Every structure of UniProt P9WH87
- Every structure of UniProt P9WH85
- Every structure of UniProt P9WH83
- Every structure of UniProt P9WH81
- Every structure of UniProt P9WH79
- Every structure of UniProt A0A0T9D5H2
- Every structure of UniProt A0A045HTP7
- Every structure of UniProt P9WHD7
- Every structure of UniProt P9WHD5
- Every structure of UniProt P9WHD3
- Every structure of UniProt P9WHD1
- Every structure of UniProt P9WHC9
- Every structure of UniProt P9WHC5
- Every structure of UniProt P9WHC3
- Every structure of UniProt P9WHC1
- Every structure of UniProt P9WHB9
- Every structure of UniProt P9WHB7
- Every structure of UniProt P9WHB5
- Every structure of UniProt P9WHB3
- Every structure of UniProt A0A045IDB8
- Every structure of UniProt P9WHA7
- Every structure of UniProt P9WHA3
- Every structure of UniProt P9WH37
- Every structure of UniProt P9WH35
- Every structure of UniProt P9WH33
- Every structure of UniProt P9WH31
- Every structure of UniProt P9WH29
- Every structure of UniProt P9WH27
- Every structure of UniProt P9WH25
- Every structure of UniProt P9WH67
- Every structure of UniProt P9WH65
- Every structure of UniProt P9WH63
- Every structure of UniProt P9WH61
- Every structure of UniProt P9WH57
- Every structure of UniProt P9WH55
- Every structure of UniProt P9WH53
- Every structure of UniProt P9WH51
- Every structure of UniProt P9WH49
- Every structure of UniProt P9WH45
- Every structure of UniProt P9WH41
- Every structure of UniProt P9WQK3
- Elsewhere: RCSB PDB 7MSH · PDBe 7MSH · UniProt P9WH99 · UniProt P9WH95 · UniProt P9WH93 · UniProt P9WH91 · UniProt P9WH89 · UniProt P9WHA1 · UniProt A0A3E0UTA6 · UniProt P9WHC7 · UniProt P9WHA5 · UniProt P9WH87 · UniProt P9WH85 · UniProt P9WH83 · UniProt P9WH81 · UniProt P9WH79 · UniProt A0A0T9D5H2 · UniProt A0A045HTP7 · UniProt P9WHD7 · UniProt P9WHD5 · UniProt P9WHD3 · UniProt P9WHD1 · UniProt P9WHC9 · UniProt P9WHC5 · UniProt P9WHC3 · UniProt P9WHC1 · UniProt P9WHB9 · UniProt P9WHB7 · UniProt P9WHB5 · UniProt P9WHB3 · UniProt A0A045IDB8 · UniProt P9WHA7 · UniProt P9WHA3 · UniProt P9WH37 · UniProt P9WH35 · UniProt P9WH33 · UniProt P9WH31 · UniProt P9WH29 · UniProt P9WH27 · UniProt P9WH25 · UniProt P9WH67 · UniProt P9WH65 · UniProt P9WH63 · UniProt P9WH61 · UniProt P9WH57 · UniProt P9WH55 · UniProt P9WH53 · UniProt P9WH51 · UniProt P9WH49 · UniProt P9WH45 · UniProt P9WH41 · UniProt P9WQK3
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