Research workbench
Crystal structure of et-ehred complex
Analyse Crystal structure of et-ehred complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3A8J
- Type
- protein
- Length
- 1,707 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
- 13 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Aminomethyltransferase (EC 2.1.2.10) | protein | 363 | 26% helix, 36% strand | P27248 |
| E | Glycine cleavage system H protein | protein | 127 | 24% helix, 34% strand | P0A6T9 |
| F | Glycine cleavage system H protein | protein | 128 | 24% helix, 34% strand | P0A6T9 |
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1170 | 0.82 | 0.83 | 137 | empty |
| 2 | 467 | 0.75 | 0.83 | 68 | empty |
| 3 | 406 | 0.73 | 0.83 | 55 | empty |
| 4 | 457 | 0.72 | 0.82 | 64 | empty |
| 5 | 110 | 0.50 | 0.82 | 28 | empty |
Interfaces
6 interfaces between chains.
- B–D · 975 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 960 Ų buried · 21 hydrogen bonds · protein-protein
- B–F · 867 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 836 Ų buried · 13 hydrogen bonds · protein-protein
- B–E · 349 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 3A8J · Crystal Structure of ET-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 E 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 3A8J · PDBe 3A8J · UniProt P27248 · UniProt P0A6T9
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