Research workbench
Crystal structure of ugpb from mycobacterium tuberculosis in complex with glycerophosphocholine
Analyse Crystal structure of ugpb from mycobacterium tuberculosis in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6R1B
- Type
- protein
- Length
- 1,555 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative sn-glycerol-3-phosphate-binding lipoprotein ugpb
- UniProt
- A0A0U0RXC0
- Ligands
- CH5, MG
- Pockets
- 13 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative sn-glycerol-3-phosphate-binding lipoprotein ugpb | protein | 394 | 52% helix, 16% strand | A0A0U0RXC0 |
| B | Putative sn-glycerol-3-phosphate-binding lipoprotein ugpb | protein | 395 | 52% helix, 16% strand | A0A0U0RXC0 |
| C | Putative sn-glycerol-3-phosphate-binding lipoprotein ugpb | protein | 384 | 48% helix, 17% strand | A0A0U0RXC0 |
| D | Putative sn-glycerol-3-phosphate-binding lipoprotein ugpb | protein | 382 | 48% helix, 17% strand | A0A0U0RXC0 |
Ligands and binding sites
- CH5 · 2-(((R)-2,3-dihydroxypropyl)phosphoryloxy)-N,N,N-trimethylethanaminium · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 720 | 0.77 | 0.82 | 84 | CH5, GOL |
| 2 | 488 | 0.73 | 0.82 | 57 | CH5 |
| 3 | 590 | 0.71 | 0.80 | 56 | CH5 |
| 4 | 545 | 0.70 | 0.79 | 56 | CH5 |
| 5 | 398 | 0.58 | 0.75 | 52 | MG |
Interfaces
2 interfaces between chains.
- B–C · 683 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 156 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (methylation).
Compared structures
- 6R1B · Crystal structure of UgpB from Mycobacterium tuberculosis in complex with… · the same entry in another collection · chain A against A, 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 A0A0U0RXC0
- Elsewhere: RCSB PDB 6R1B · PDBe 6R1B · UniProt A0A0U0RXC0
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