Research workbench
Crystal structure of ETD97N-ehred complex
Analyse Crystal structure of ETD97N-ehred complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3A8K
- Type
- protein
- Length
- 1,702 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminomethyltransferase; Glycine cleavage system H protein
- EC
- 2.1.2.10
- UniProt
- P27248, P0A6T9
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Aminomethyltransferase (EC 2.1.2.10) | protein | 363 | 26% helix, 35% strand | P27248 |
| C, D | Aminomethyltransferase (EC 2.1.2.10) | protein | 362 | 26% helix, 36% strand | P27248 |
| E, F | Glycine cleavage system H protein | protein | 126 | 23% helix, 35% strand | P0A6T9 |
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1082 | 0.81 | 0.82 | 121 | empty |
| 2 | 479 | 0.73 | 0.82 | 70 | empty |
| 3 | 420 | 0.71 | 0.82 | 59 | empty |
| 4 | 340 | 0.67 | 0.81 | 46 | empty |
| 5 | 94 | 0.48 | 0.82 | 28 | empty |
Interfaces
6 interfaces between chains.
- B–D · 954 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 943 Ų buried · 21 hydrogen bonds · protein-protein
- B–F · 923 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 884 Ų buried · 13 hydrogen bonds · protein-protein
- B–E · 325 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 3A8K · Crystal Structure of ETD97N-EHred complex · the same entry in another collection · chain F against F, TM-score 1.00
- P27248 · AlphaFold monomer V2.0 prediction for aminomethyltransferase (P27248) · a predicted model of the same protein · chain C against A, TM-score 0.99
- P0A6T9 · AlphaFold monomer V2.0 prediction for glycine cleavage system H protein (P0A6T9) · a predicted model of the same protein · chain F against A, TM-score 0.97
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 P27248
- Every structure of UniProt P0A6T9
- Elsewhere: RCSB PDB 3A8K · PDBe 3A8K · UniProt P27248 · UniProt P0A6T9
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