MolNFT v1 · #126382 · protein
Crystal structure of N-terminally tagged ubid from E. COLI reconstituted with prfmn cofactor
5M1D · 3-octaprenyl-4-hydroxybenzoate carboxy-lyase: “Crystal structure of N-terminally tagged ubid from E. COLI reconstituted with prfmn cofactor”. X-ray diffraction, 4 ligands (4LU, MN, NA), 17 pockets (best druggability 0.85). MolNFT v1…
- PDB
- 5M1D
- Type
- protein
- Length
- 1,393 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-octaprenyl-4-hydroxybenzoate carboxy-lyase
- EC
- 4.1.1.98
- UniProt
- P0AAB5
- Ligands
- 4LU, MN, NA, SO4
- Pockets
- 17 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-octaprenyl-4-hydroxybenzoate carboxy-lyase (EC 4.1.1.98) | protein | 469 | 30% helix, 28% strand | P0AAB5 |
| B | 3-octaprenyl-4-hydroxybenzoate carboxy-lyase (EC 4.1.1.98) | protein | 465 | 31% helix, 28% strand | P0AAB5 |
| C | 3-octaprenyl-4-hydroxybenzoate carboxy-lyase (EC 4.1.1.98) | protein | 459 | 30% helix, 28% strand | P0AAB5 |
Ligands and binding sites
- 4LU · 1-deoxy-5-O-phosphono-1-(3,3,4,5-tetramethyl-9,11-dioxo-2,3,8,9,10,11-hexahydro-7H-quinolino[1,8-fg]pteridin-12-ium-7-yl)-D-ribitol · ligand · 3 copies · chains A, B, C
- MN · Manganese (II) ion · metal · 3 copies · chains A, B, C
- NA · Sodium ion · metal · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 994 | 0.85 | 0.86 | 75 | 4LU, NA |
| 2 | 1091 | 0.82 | 0.83 | 73 | 4LU, NA, SO4 |
| 3 | 78 | 0.79 | 0.99 | 18 | empty |
| 4 | 427 | 0.74 | 0.84 | 59 | 4LU |
| 5 | 98 | 0.48 | 0.81 | 22 | empty |
Interfaces
2 interfaces between chains.
- A–B · 4287 Ų buried · 63 hydrogen bonds · protein-protein
- A–C · 1254 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5M1D · Crystal structure of N-terminally tagged UbiD from E. coli reconstituted with prFMN… · the same entry in another collection · chain A against A, TM-score 1.00
- P0AAB5 · AlphaFold monomer V2.0 prediction for 3-octaprenyl-4-hydroxybenzoate carboxy-lyase… · a predicted model of the same protein · chain C 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 P0AAB5
- Elsewhere: RCSB PDB 5M1D · PDBe 5M1D · UniProt P0AAB5
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