Research workbench
Crystal structure of phosphoribosylglycinamide formyltransferase from anaplasma phagocytophilum
Analyse Crystal structure of phosphoribosylglycinamide formyltransferase from anaplasma… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KCQ
- Type
- protein
- Length
- 824 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoribosylglycinamide formyltransferase
- EC
- 2.1.2.2
- UniProt
- Q2GLA4
- Pockets
- 9 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoribosylglycinamide formyltransferase (EC 2.1.2.2) | protein | 207 | 31% helix, 26% strand | Q2GLA4 |
| B | Phosphoribosylglycinamide formyltransferase (EC 2.1.2.2) | protein | 204 | 31% helix, 25% strand | Q2GLA4 |
| C | Phosphoribosylglycinamide formyltransferase (EC 2.1.2.2) | protein | 209 | 31% helix, 26% strand | Q2GLA4 |
| D | Phosphoribosylglycinamide formyltransferase (EC 2.1.2.2) | protein | 204 | 31% helix, 25% strand | Q2GLA4 |
Ligands and binding sites
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 558 | 0.69 | 0.78 | 57 | GOL |
| 2 | 414 | 0.65 | 0.79 | 39 | GOL |
| 3 | 389 | 0.64 | 0.78 | 42 | GOL |
| 4 | 359 | 0.63 | 0.79 | 40 | GOL |
| 5 | 338 | 0.51 | 0.72 | 38 | empty |
Interfaces
3 interfaces between chains.
- A–C · 423 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 399 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 178 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3KCQ · Crystal structure of phosphoribosylglycinamide formyltransferase from anaplasma… · the same entry in another collection · chain B against B, 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 Q2GLA4
- Elsewhere: RCSB PDB 3KCQ · PDBe 3KCQ · UniProt Q2GLA4
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