Research workbench
Structure of mature human mitochondrial ribosome large subunit in complex with GTPBP6 (PTC conformation 1).
Analyse Structure of mature human mitochondrial ribosome large subunit in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OF4
- Type
- protein + RNA
- Length
- 9,839 residues
- Chains
- 53
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.7
- Source
- Homo sapiens
- Molecule
- 39S ribosomal protein L32, mitochondrial; 39S ribosomal protein L33, mitochondrial; 39S…
- EC
- 3.1.26.-, 3.1.1.29
- UniProt
- Q9BYC8, O75394, Q9BQ48, Q9NZE8, Q9P0J6, Q9BZE1, Q96DV4, Q9NYK5, Q9NQ50, Q8IXM3, O43824, Q5T653, P09001, Q9BYD3, Q9BYD2, Q7Z7H8, Q9Y3B7, Q9BYD1, Q6P1L8, Q9P015, Q9NX20, Q9NRX2, Q9H0U6, P49406, Q9BYC9, Q7Z2W9, Q9NWU5, Q16540, Q96A35, Q9P0M9, Q13084, Q9HD33, Q8TCC3, Q9Y6G3, Q8N983, Q9H9J2, Q9BRJ2, Q9H2W6, Q96GC5, Q13405, Q8N5N7, Q4U2R6, Q86TS9, Q96EL3, Q6P161, Q7Z7F7, Q9BQC6, Q14197, Q8TAE8, Q9NVS2, Q9NP92
- Ligands
- GTP, MG, ZN
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · resolution 2.7 · 53 distinct chains · 34% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 0 | 39S ribosomal protein L32, mitochondrial | protein | 108 | 29% helix, 15% strand | Q9BYC8 |
| 1 | 39S ribosomal protein L33, mitochondrial | protein | 52 | 0% helix, 65% strand | O75394 |
| 2 | 39S ribosomal protein L34, mitochondrial | protein | 45 | 60% helix, 0% strand | Q9BQ48 |
| 3 | 39S ribosomal protein L35, mitochondrial | protein | 95 | 34% helix, 9% strand | Q9NZE8 |
| 4 | 39S ribosomal protein L36, mitochondrial | protein | 37 | 8% helix, 38% strand | Q9P0J6 |
| 5 | 39S ribosomal protein L37, mitochondrial | protein | 392 | 26% helix, 26% strand | Q9BZE1 |
| 6 | 39S ribosomal protein L38, mitochondrial | protein | 324 | 31% helix, 21% strand | Q96DV4 |
| 7 | 39S ribosomal protein L39, mitochondrial | protein | 287 | 41% helix, 27% strand | Q9NYK5 |
| 8 | 39S ribosomal protein L40, mitochondrial | protein | 77 | 69% helix, 3% strand | Q9NQ50 |
| 9 | 39S ribosomal protein L41, mitochondrial | protein | 117 | 25% helix, 9% strand | Q8IXM3 |
| A | 16S ribosomal RNA | rna | 1463 | — | — |
| B | mitochondrial tRNAVal | rna | 56 | — | — |
| C | Putative GTP-binding protein 6 | protein | 422 | 45% helix, 20% strand | O43824 |
| D | 39S ribosomal protein L2, mitochondrial | protein | 236 | 8% helix, 29% strand | Q5T653 |
| E | 39S ribosomal protein L3, mitochondrial | protein | 305 | 17% helix, 30% strand | P09001 |
| F | 39S ribosomal protein L4, mitochondrial | protein | 250 | 30% helix, 15% strand | Q9BYD3 |
| H | 39S ribosomal protein L9, mitochondrial | protein | 95 | 29% helix, 29% strand | Q9BYD2 |
| I | 39S ribosomal protein L10, mitochondrial | protein | 158 | 45% helix, 12% strand | Q7Z7H8 |
| J | 39S ribosomal protein L11, mitochondrial | protein | 140 | 36% helix, 14% strand | Q9Y3B7 |
| K | 39S ribosomal protein L13, mitochondrial | protein | 177 | 38% helix, 16% strand | Q9BYD1 |
| L | 39S ribosomal protein L14, mitochondrial | protein | 115 | 14% helix, 31% strand | Q6P1L8 |
| M | 39S ribosomal protein L15, mitochondrial | protein | 287 | 34% helix, 11% strand | Q9P015 |
| N | 39S ribosomal protein L16, mitochondrial | protein | 205 | 31% helix, 23% strand | Q9NX20 |
| O | 39S ribosomal protein L17, mitochondrial | protein | 152 | 51% helix, 11% strand | Q9NRX2 |
| P | 39S ribosomal protein L18, mitochondrial | protein | 141 | 34% helix, 18% strand | Q9H0U6 |
| Q | 39S ribosomal protein L19, mitochondrial | protein | 217 | 31% helix, 24% strand | P49406 |
| R | 39S ribosomal protein L20, mitochondrial | protein | 140 | 71% helix, 1% strand | Q9BYC9 |
| S | 39S ribosomal protein L21, mitochondrial | protein | 156 | 13% helix, 44% strand | Q7Z2W9 |
| T | 39S ribosomal protein L22, mitochondrial | protein | 166 | 36% helix, 25% strand | Q9NWU5 |
| U | 39S ribosomal protein L23, mitochondrial | protein | 139 | 17% helix, 22% strand | Q16540 |
| V | 39S ribosomal protein L24, mitochondrial | protein | 191 | 12% helix, 24% strand | Q96A35 |
| W | 39S ribosomal protein L27, mitochondrial | protein | 109 | 8% helix, 39% strand | Q9P0M9 |
| X | 39S ribosomal protein L28, mitochondrial | protein | 243 | 48% helix, 16% strand | Q13084 |
| Y | 39S ribosomal protein L47, mitochondrial | protein | 176 | 59% helix, 7% strand | Q9HD33 |
| Z | 39S ribosomal protein L30, mitochondrial | protein | 120 | 30% helix, 19% strand | Q8TCC3 |
| a | 39S ribosomal protein L42, mitochondrial | protein | 82 | 29% helix, 13% strand | Q9Y6G3 |
| b | 39S ribosomal protein L43, mitochondrial | protein | 148 | 24% helix, 21% strand | Q8N983 |
| c | 39S ribosomal protein L44, mitochondrial (EC 3.1.26.-) | protein | 275 | 59% helix, 9% strand | Q9H9J2 |
| d | 39S ribosomal protein L45, mitochondrial | protein | 208 | 22% helix, 25% strand | Q9BRJ2 |
| e | 39S ribosomal protein L46, mitochondrial | protein | 197 | 27% helix, 23% strand | Q9H2W6 |
| f | 39S ribosomal protein L48, mitochondrial | protein | 105 | 31% helix, 20% strand | Q96GC5 |
| g | 39S ribosomal protein L49, mitochondrial | protein | 129 | 24% helix, 23% strand | Q13405 |
| h | 39S ribosomal protein L50, mitochondrial | protein | 105 | 48% helix, 9% strand | Q8N5N7 |
| i | 39S ribosomal protein L51, mitochondrial | protein | 97 | 47% helix, 1% strand | Q4U2R6 |
| j | 39S ribosomal protein L52, mitochondrial | protein | 84 | 68% helix, 5% strand | Q86TS9 |
| k | 39S ribosomal protein L53, mitochondrial | protein | 80 | 36% helix, 23% strand | Q96EL3 |
| l | 39S ribosomal protein L54, mitochondrial | protein | 23 | 83% helix, 0% strand | Q6P161 |
| m | 39S ribosomal protein L55, mitochondrial | protein | 45 | 0% helix, 29% strand | Q7Z7F7 |
| o | Ribosomal protein 63, mitochondrial | protein | 94 | 55% helix, 1% strand | Q9BQC6 |
| p | Peptidyl-tRNA hydrolase ICT1, mitochondrial (EC 3.1.1.29) | protein | 127 | 40% helix, 15% strand | Q14197 |
| q | Growth arrest and DNA damage-inducible proteins-interacting protein 1 | protein | 120 | 70% helix, 1% strand | Q8TAE8 |
| r | 39S ribosomal protein S18a, mitochondrial | protein | 157 | 26% helix, 15% strand | Q9NVS2 |
| s | 39S ribosomal protein S30, mitochondrial | protein | 370 | 36% helix, 22% strand | Q9NP92 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 3 copies · chains A, Y, 3, C
- MG · Magnesium ion · metal · 89 copies · chains A, F, d, Q, M, O, 2, U, E, T, W, o, L, R, C, g
- ZN · Zinc ion · metal · 3 copies · chains 0, 4, I, 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 | 1180 | 0.89 | 0.92 | 114 | MG |
| 2 | 958 | 0.88 | 0.91 | 109 | MG |
| 3 | 1021 | 0.88 | 0.90 | 119 | MG |
| 4 | 1073 | 0.87 | 0.89 | 85 | empty |
| 5 | 846 | 0.87 | 0.90 | 81 | MG |
Interfaces
206 interfaces between chains.
- A–E · 5174 Ų buried · 108 hydrogen bonds · protein-nucleic
- A–D · 4871 Ų buried · 140 hydrogen bonds · protein-nucleic
- A–M · 4151 Ų buried · 129 hydrogen bonds · protein-nucleic
- A–F · 3670 Ų buried · 70 hydrogen bonds · protein-nucleic
- A–C · 3503 Ų buried · 59 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 3 modified (nucleotide modification).
Compared structures
- Q9NP92 · AlphaFold monomer V2.0 prediction for 39S ribosomal protein S30, mitochondrial (Q9NP92) · a predicted model of the same protein · chain s against A, TM-score 0.99
- Q9H9J2 · AlphaFold monomer V2.0 prediction for 39S ribosomal protein L44, mitochondrial (Q9H9J2) · a predicted model of the same protein · chain c against A, TM-score 0.99
- Q5T653 · AlphaFold monomer V2.0 prediction for 39S ribosomal protein L2, mitochondrial (Q5T653) · a predicted model of the same protein · chain D against A, TM-score 0.99
- Q9NX20 · AlphaFold monomer V2.0 prediction for 39S ribosomal protein L16, mitochondrial (Q9NX20) · a predicted model of the same protein · chain N against A, TM-score 0.99
- P49406 · AlphaFold monomer V2.0 prediction for 39S ribosomal protein L19, mitochondrial (P49406) · a predicted model of the same protein · chain Q against A, TM-score 0.99
- P09001 · AlphaFold monomer V2.0 prediction for 39S ribosomal protein L3, mitochondrial (P09001) · a predicted model of the same protein · chain E against A, TM-score 0.99
- Q9NYK5 · AlphaFold monomer V2.0 prediction for 39S ribosomal protein L39, mitochondrial (Q9NYK5) · a predicted model of the same protein · chain 7 against A, TM-score 0.99
- Q13084 · AlphaFold monomer V2.0 prediction for 39S ribosomal protein L28, mitochondrial (Q13084) · a predicted model of the same protein · chain X against A, TM-score 0.99
- Q9BZE1 · AlphaFold monomer V2.0 prediction for 39S ribosomal protein L37, mitochondrial (Q9BZE1) · a predicted model of the same protein · chain 5 against A, TM-score 0.99
- Q8N983 · AlphaFold monomer V2.0 prediction for 39S ribosomal protein L43, mitochondrial (Q8N983) · a predicted model of the same protein · chain b against A, TM-score 0.99
- Q9BYD3 · AlphaFold monomer V2.0 prediction for 39S ribosomal protein L4, mitochondrial (Q9BYD3) · a predicted model of the same protein · chain F against A, TM-score 0.99
- Q9NRX2 · AlphaFold monomer V2.0 prediction for 39S ribosomal protein L17, mitochondrial (Q9NRX2) · a predicted model of the same protein · chain O against A, TM-score 0.99
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 Q9BYC8
- Every structure of UniProt O75394
- Every structure of UniProt Q9BQ48
- Every structure of UniProt Q9NZE8
- Every structure of UniProt Q9P0J6
- Every structure of UniProt Q9BZE1
- Every structure of UniProt Q96DV4
- Every structure of UniProt Q9NYK5
- Every structure of UniProt Q9NQ50
- Every structure of UniProt Q8IXM3
- Every structure of UniProt O43824
- Every structure of UniProt Q5T653
- Every structure of UniProt P09001
- Every structure of UniProt Q9BYD3
- Every structure of UniProt Q9BYD2
- Every structure of UniProt Q7Z7H8
- Every structure of UniProt Q9Y3B7
- Every structure of UniProt Q9BYD1
- Every structure of UniProt Q6P1L8
- Every structure of UniProt Q9P015
- Every structure of UniProt Q9NX20
- Every structure of UniProt Q9NRX2
- Every structure of UniProt Q9H0U6
- Every structure of UniProt P49406
- Every structure of UniProt Q9BYC9
- Every structure of UniProt Q7Z2W9
- Every structure of UniProt Q9NWU5
- Every structure of UniProt Q16540
- Every structure of UniProt Q96A35
- Every structure of UniProt Q9P0M9
- Every structure of UniProt Q13084
- Every structure of UniProt Q9HD33
- Every structure of UniProt Q8TCC3
- Every structure of UniProt Q9Y6G3
- Every structure of UniProt Q8N983
- Every structure of UniProt Q9H9J2
- Every structure of UniProt Q9BRJ2
- Every structure of UniProt Q9H2W6
- Every structure of UniProt Q96GC5
- Every structure of UniProt Q13405
- Every structure of UniProt Q8N5N7
- Every structure of UniProt Q4U2R6
- Every structure of UniProt Q86TS9
- Every structure of UniProt Q96EL3
- Every structure of UniProt Q6P161
- Every structure of UniProt Q7Z7F7
- Every structure of UniProt Q9BQC6
- Every structure of UniProt Q14197
- Every structure of UniProt Q8TAE8
- Every structure of UniProt Q9NVS2
- Every structure of UniProt Q9NP92
- Elsewhere: RCSB PDB 7OF4 · PDBe 7OF4 · UniProt Q9BYC8 · UniProt O75394 · UniProt Q9BQ48 · UniProt Q9NZE8 · UniProt Q9P0J6 · UniProt Q9BZE1 · UniProt Q96DV4 · UniProt Q9NYK5 · UniProt Q9NQ50 · UniProt Q8IXM3 · UniProt O43824 · UniProt Q5T653 · UniProt P09001 · UniProt Q9BYD3 · UniProt Q9BYD2 · UniProt Q7Z7H8 · UniProt Q9Y3B7 · UniProt Q9BYD1 · UniProt Q6P1L8 · UniProt Q9P015 · UniProt Q9NX20 · UniProt Q9NRX2 · UniProt Q9H0U6 · UniProt P49406 · UniProt Q9BYC9 · UniProt Q7Z2W9 · UniProt Q9NWU5 · UniProt Q16540 · UniProt Q96A35 · UniProt Q9P0M9 · UniProt Q13084 · UniProt Q9HD33 · UniProt Q8TCC3 · UniProt Q9Y6G3 · UniProt Q8N983 · UniProt Q9H9J2 · UniProt Q9BRJ2 · UniProt Q9H2W6 · UniProt Q96GC5 · UniProt Q13405 · UniProt Q8N5N7 · UniProt Q4U2R6 · UniProt Q86TS9 · UniProt Q96EL3 · UniProt Q6P161 · UniProt Q7Z7F7 · UniProt Q9BQC6 · UniProt Q14197 · UniProt Q8TAE8 · UniProt Q9NVS2 · UniProt Q9NP92
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