Research workbench
Structure of human mitochondrial translation initiation factor 3 bound to the small ribosomal subunit-class-II
Analyse Structure of human mitochondrial translation initiation factor 3 bound to the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NEQ
- Type
- protein + RNA
- Length
- 6,608 residues
- Chains
- 32
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 28S ribosomal RNA, mitochondrial; 28S ribosomal protein S24, mitochondrial; 28S ribosomal…
- UniProt
- Q2M2T7, Q2KID9, Q29RU1, P82915, P82916, P82649, P82669, Q3SZ86, Q32PI8, P82929, P82918, Q3T040, Q58DQ5, P82670, Q6B860, A6QQP1, P82925, P82926, Q2YDF6, Q2HJE8, Q2KI62, P82923, P82931, P82911, P82913, P82917, P82920, Q2NL27, P82928, Q0VCJ1, Q9H2K0
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 32 distinct chains · 42% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 28S ribosomal RNA, mitochondrial | rna | 952 | — | — |
| C | 28S ribosomal protein S24, mitochondrial | protein | 123 | 25% helix, 19% strand | Q2M2T7 |
| E | 28S ribosomal protein S5, mitochondrial | protein | 309 | 22% helix, 17% strand | Q2KID9 |
| L | 28S ribosomal protein S12, mitochondrial | protein | 109 | 9% helix, 27% strand | Q29RU1 |
| P | 28S ribosomal protein S16, mitochondrial | protein | 116 | 35% helix, 16% strand | P82915 |
| Q | 28S ribosomal protein S17, mitochondrial | protein | 109 | 0% helix, 45% strand | P82916 |
| a | 28S ribosomal protein S22, mitochondrial | protein | 289 | 52% helix, 9% strand | P82649 |
| c | 28S ribosomal protein S25, mitochondrial | protein | 168 | 33% helix, 16% strand | P82669 |
| d | 28S ribosomal protein S26, mitochondrial | protein | 176 | 73% helix, 2% strand | Q3SZ86 |
| e | 28S ribosomal protein S27, mitochondrial | protein | 358 | 68% helix, 0% strand | Q32PI8 |
| j | 28S ribosomal protein S34, mitochondrial | protein | 213 | 26% helix, 17% strand | P82929 |
| p | 28S ribosomal protein S18B, mitochondrial | protein | 187 | 30% helix, 2% strand | P82918 |
| G | 28S ribosomal protein S7, mitochondrial | protein | 208 | 54% helix, 8% strand | Q3T040 |
| I | 28S ribosomal protein S9, mitochondrial | protein | 311 | 42% helix, 9% strand | Q58DQ5 |
| J | 28S ribosomal protein S10, mitochondrial | protein | 128 | 23% helix, 32% strand | P82670 |
| N | 28S ribosomal protein S14, mitochondrial | protein | 101 | 50% helix, 4% strand | Q6B860 |
| g | DAP3 protein | protein | 351 | 46% helix, 13% strand | A6QQP1 |
| h | 28S ribosomal protein S31, mitochondrial | protein | 103 | 52% helix, 0% strand | P82925 |
| i | 28S ribosomal protein S33, mitochondrial | protein | 98 | 50% helix, 0% strand | P82926 |
| k | 28S ribosomal protein S35, mitochondrial | protein | 275 | 40% helix, 7% strand | Q2YDF6 |
| m | Coiled-coil-helix-coiled-coil-helix domain containing 1 | protein | 118 | 31% helix, 0% strand | Q2HJE8 |
| o | Pentatricopeptide repeat domain-containing protein 3, mitochondrial | protein | 461 | 57% helix, 0% strand | Q2KI62 |
| B | 28S ribosomal protein S2, mitochondrial | protein | 217 | 39% helix, 12% strand | P82923 |
| F | 28S ribosomal protein S6, mitochondrial | protein | 124 | 23% helix, 34% strand | P82931 |
| K | 28S ribosomal protein S11, mitochondrial | protein | 136 | 24% helix, 19% strand | P82911 |
| O | 28S ribosomal protein S15, mitochondrial | protein | 173 | 65% helix, 1% strand | P82913 |
| R | 28S ribosomal protein S18C, mitochondrial | protein | 97 | 32% helix, 0% strand | P82917 |
| U | 28S ribosomal protein S21, mitochondrial | protein | 86 | 60% helix, 5% strand | P82920 |
| b | 28S ribosomal protein S23, mitochondrial | protein | 135 | 43% helix, 1% strand | Q2NL27 |
| f | 28S ribosomal protein S28, mitochondrial | protein | 98 | 11% helix, 35% strand | P82928 |
| n | Aurora kinase a interacting protein 1 | protein | 72 | 68% helix, 0% strand | Q0VCJ1 |
| z | Translation initiation factor if-3, mitochondrial | protein | 207 | 34% helix, 18% strand | Q9H2K0 |
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 | 1098 | 0.89 | 0.91 | 102 | empty |
| 2 | 810 | 0.86 | 0.89 | 75 | empty |
| 3 | 952 | 0.86 | 0.88 | 76 | empty |
| 4 | 1006 | 0.85 | 0.87 | 69 | empty |
| 5 | 1133 | 0.84 | 0.86 | 83 | empty |
Interfaces
116 interfaces between chains.
- A–O · 2614 Ų buried · 38 hydrogen bonds · protein-nucleic
- A–E · 2605 Ų buried · 36 hydrogen bonds · protein-nucleic
- A–n · 2535 Ų buried · 33 hydrogen bonds · protein-nucleic
- A–L · 2497 Ų buried · 49 hydrogen bonds · protein-nucleic
- A–N · 2339 Ų buried · 46 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6NEQ · Structure of human mitochondrial translation initiation factor 3 bound to the small… · the same entry in another collection · chain j against j, 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 Q2M2T7
- Every structure of UniProt Q2KID9
- Every structure of UniProt Q29RU1
- Every structure of UniProt P82915
- Every structure of UniProt P82916
- Every structure of UniProt P82649
- Every structure of UniProt P82669
- Every structure of UniProt Q3SZ86
- Every structure of UniProt Q32PI8
- Every structure of UniProt P82929
- Every structure of UniProt P82918
- Every structure of UniProt Q3T040
- Every structure of UniProt Q58DQ5
- Every structure of UniProt P82670
- Every structure of UniProt Q6B860
- Every structure of UniProt A6QQP1
- Every structure of UniProt P82925
- Every structure of UniProt P82926
- Every structure of UniProt Q2YDF6
- Every structure of UniProt Q2HJE8
- Every structure of UniProt Q2KI62
- Every structure of UniProt P82923
- Every structure of UniProt P82931
- Every structure of UniProt P82911
- Every structure of UniProt P82913
- Every structure of UniProt P82917
- Every structure of UniProt P82920
- Every structure of UniProt Q2NL27
- Every structure of UniProt P82928
- Every structure of UniProt Q0VCJ1
- Every structure of UniProt Q9H2K0
- Elsewhere: RCSB PDB 6NEQ · PDBe 6NEQ · UniProt Q2M2T7 · UniProt Q2KID9 · UniProt Q29RU1 · UniProt P82915 · UniProt P82916 · UniProt P82649 · UniProt P82669 · UniProt Q3SZ86 · UniProt Q32PI8 · UniProt P82929 · UniProt P82918 · UniProt Q3T040 · UniProt Q58DQ5 · UniProt P82670 · UniProt Q6B860 · UniProt A6QQP1 · UniProt P82925 · UniProt P82926 · UniProt Q2YDF6 · UniProt Q2HJE8 · UniProt Q2KI62 · UniProt P82923 · UniProt P82931 · UniProt P82911 · UniProt P82913 · UniProt P82917 · UniProt P82920 · UniProt Q2NL27 · UniProt P82928 · UniProt Q0VCJ1 · UniProt Q9H2K0
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