Research workbench
L-rhamnulose-1-phosphate aldolase from escherichia COLI
Analyse L-rhamnulose-1-phosphate aldolase from escherichia COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1GT7
- Type
- protein
- Length
- 5,480 residues
- Chains
- 20
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rhamnulose-1-phosphate aldolase
- EC
- 4.1.2.19
- UniProt
- P32169
- Ligands
- PGH, ZN
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T | Rhamnulose-1-phosphate aldolase (EC 4.1.2.19) | protein | 274 | 45% helix, 17% strand | P32169 |
Ligands and binding sites
- PGH · Phosphoglycolohydroxamic acid · ligand · 20 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
- ZN · Zinc ion · metal · 20 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 844 | 0.85 | 0.87 | 85 | ZN, PGH |
| 2 | 966 | 0.85 | 0.86 | 99 | PGH, ZN |
| 3 | 992 | 0.85 | 0.86 | 100 | PGH, ZN |
| 4 | 1093 | 0.84 | 0.85 | 122 | PGH, ZN |
| 5 | 1027 | 0.82 | 0.83 | 67 | empty |
Interfaces
32 interfaces between chains.
- O–P · 1446 Ų buried · 21 hydrogen bonds · protein-protein
- J–K · 1445 Ų buried · 21 hydrogen bonds · protein-protein
- G–H · 1443 Ų buried · 21 hydrogen bonds · protein-protein
- K–L · 1443 Ų buried · 21 hydrogen bonds · protein-protein
- S–T · 1441 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 1GT7 · L-rhamnulose-1-phosphate aldolase from Escherichia coli · the same entry in another collection · chain T against T, 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 P32169
- Elsewhere: RCSB PDB 1GT7 · PDBe 1GT7 · UniProt P32169
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