Research workbench
Crystal structure of project MJ0051 from methanocaldococcus jannaschii dsm 2661
Analyse Crystal structure of project MJ0051 from methanocaldococcus jannaschii dsm 2661 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZV3
- Type
- protein
- Length
- 1,005 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidyl-tRNA hydrolase
- EC
- 3.1.1.29
- UniProt
- Q60363
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 45% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidyl-tRNA hydrolase (EC 3.1.1.29) | protein | 108 | 49% helix, 28% strand | Q60363 |
| B, D, E, F | Peptidyl-tRNA hydrolase (EC 3.1.1.29) | protein | 115 | 44% helix, 26% strand | Q60363 |
| C | Peptidyl-tRNA hydrolase (EC 3.1.1.29) | protein | 111 | 47% helix, 27% strand | Q60363 |
| G | Peptidyl-tRNA hydrolase (EC 3.1.1.29) | protein | 110 | 45% helix, 26% strand | Q60363 |
| H | Peptidyl-tRNA hydrolase (EC 3.1.1.29) | protein | 103 | 37% helix, 25% strand | Q60363 |
| I | Peptidyl-tRNA hydrolase (EC 3.1.1.29) | protein | 113 | 46% helix, 27% strand | Q60363 |
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 818 | 0.79 | 0.82 | 85 | empty |
| 2 | 708 | 0.75 | 0.81 | 59 | empty |
| 3 | 197 | 0.52 | 0.77 | 25 | empty |
| 4 | 74 | 0.46 | 0.83 | 16 | empty |
| 5 | 61 | 0.42 | 0.82 | 13 | empty |
Interfaces
18 interfaces between chains.
- C–D · 995 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 991 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 981 Ų buried · 4 hydrogen bonds · protein-protein
- G–H · 958 Ų buried · 4 hydrogen bonds · protein-protein
- B–F · 858 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 2ZV3 · Crystal structure of project MJ0051 from Methanocaldococcus jannaschii DSM 2661 · the same entry in another collection · chain I against I, TM-score 1.00
- Q60363 · AlphaFold monomer V2.0 prediction for peptidyl-tRNA hydrolase (Q60363) · a predicted model of the same protein · chain A 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 Q60363
- Elsewhere: RCSB PDB 2ZV3 · PDBe 2ZV3 · UniProt Q60363
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