Research workbench
Crystal structure of a putative amino-acid aminotransferase (NP_104211.1) from mesorhizobium loti at 2.30 a resolution
Analyse Crystal structure of a putative amino-acid aminotransferase (NP_104211.1) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QQM
- Type
- protein
- Length
- 1,686 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MLR3007 protein
- UniProt
- Q98H69
- Ligands
- IOD, CL
- Pockets
- 20 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 26% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F, G | MLR3007 protein | protein | 215 | 25% helix, 32% strand | Q98H69 |
| B, E, H | MLR3007 protein | protein | 207 | 26% helix, 31% strand | Q98H69 |
| C | MLR3007 protein | protein | 209 | 26% helix, 32% strand | Q98H69 |
| D | MLR3007 protein | protein | 211 | 26% helix, 31% strand | Q98H69 |
Ligands and binding sites
- IOD · Iodide ion · ion · 26 copies · chains A, B, C, D, H, E, F, G
- CL · Chloride ion · ion · 14 copies · chains A, D, E, G, H
- EDO · 1,2-ethanediol · additive · 50 copies · chains A, B, C, E, D, H, F, G
- PEG · Di(hydroxyethyl)ether · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 447 | 0.68 | 0.80 | 52 | CL |
| 2 | 617 | 0.67 | 0.76 | 36 | empty |
| 3 | 589 | 0.66 | 0.76 | 45 | EDO |
| 4 | 304 | 0.64 | 0.80 | 42 | IOD, EDO |
| 5 | 505 | 0.63 | 0.76 | 51 | EDO, IOD |
Interfaces
13 interfaces between chains.
- E–F · 1069 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 1020 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 1016 Ų buried · 36 hydrogen bonds · protein-protein
- G–H · 1012 Ų buried · 29 hydrogen bonds · protein-protein
- D–E · 599 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered, cofactor).
Compared structures
- 3QQM · Crystal structure of a Putative amino-acid aminotransferase (NP_104211.1) from… · the same entry in another collection · chain A against A, 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 Q98H69
- Elsewhere: RCSB PDB 3QQM · PDBe 3QQM · UniProt Q98H69
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