MolNFT v1 · #31178 · protein
Crystal structure of 1-pyrroline-5-carboxylate reductase from human pathogen streptococcus pyogenes
2AMF: “Crystal structure of 1-pyrroline-5-carboxylate reductase from human pathogen streptococcus pyogenes”. X-ray diffraction, 2 ligands (PRO, NA), 11 pockets (best druggability 0.73). MolNFT v1 #31178 on GenesisL1: 3D structure, binding…
- PDB
- 2AMF
- Type
- protein
- Length
- 1,287 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 1-pyrroline-5-carboxylate reductase
- EC
- 1.2.1.5
- Ligands
- PRO, NA
- Pockets
- 11 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 58% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 1-pyrroline-5-carboxylate reductase (EC 1.2.1.5) | protein | 257 | 58% helix, 14% strand | — |
| C | 1-pyrroline-5-carboxylate reductase (EC 1.2.1.5) | protein | 256 | 59% helix, 13% strand | — |
| D | 1-pyrroline-5-carboxylate reductase (EC 1.2.1.5) | protein | 258 | 58% helix, 14% strand | — |
| E | 1-pyrroline-5-carboxylate reductase (EC 1.2.1.5) | protein | 259 | 59% helix, 14% strand | — |
Ligands and binding sites
- PRO · Proline · ligand · 10 copies · chains A, D, B, C, E
- NA · Sodium ion · metal · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 454 | 0.73 | 0.82 | 57 | PRO |
| 2 | 512 | 0.73 | 0.81 | 61 | PRO |
| 3 | 296 | 0.73 | 0.86 | 42 | PRO |
| 4 | 297 | 0.72 | 0.86 | 40 | PRO |
| 5 | 441 | 0.57 | 0.73 | 53 | empty |
Interfaces
8 interfaces between chains.
- A–D · 4508 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 4460 Ų buried · 34 hydrogen bonds · protein-protein
- B–D · 412 Ų buried · 0 hydrogen bonds · protein-protein
- A–E · 409 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 381 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2AMF · Crystal structure of 1-Pyrroline-5-Carboxylate Reductase from Human Pathogen… · the same entry in another collection · chain E against E, 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
- Elsewhere: RCSB PDB 2AMF · PDBe 2AMF
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