MolNFT v1 · #65109 · protein
Crystal structure of E. COLI lsrf in complex with ribulose-5-phosphate
3GND · Aldolase lsrf: “Crystal structure of E. COLI lsrf in complex with ribulose-5-phosphate”. X-ray diffraction, 1 ligand (5RP), 20 pockets (best druggability 0.71). MolNFT v1 #65109 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3GND
- Type
- protein
- Length
- 5,520 residues
- Chains
- 20
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aldolase lsrf
- EC
- 4.1.2.-
- UniProt
- P76143
- Ligands
- 5RP
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 14% 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 | Aldolase lsrf (EC 4.1.2.-) | protein | 276 | 43% helix, 14% strand | P76143 |
Ligands and binding sites
- 5RP · Ribulose-5-phosphate · ligand · 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 | 854 | 0.71 | 0.76 | 71 | 5RP |
| 2 | 160 | 0.66 | 0.87 | 24 | 5RP |
| 3 | 158 | 0.66 | 0.87 | 26 | 5RP |
| 4 | 168 | 0.65 | 0.86 | 27 | 5RP |
| 5 | 152 | 0.65 | 0.87 | 25 | 5RP |
Interfaces
41 interfaces between chains.
- C–I · 2165 Ų buried · 36 hydrogen bonds · protein-protein
- E–G · 2152 Ų buried · 40 hydrogen bonds · protein-protein
- B–J · 2125 Ų buried · 36 hydrogen bonds · protein-protein
- A–F · 2116 Ų buried · 35 hydrogen bonds · protein-protein
- D–H · 2115 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 3GND · Crystal Structure of E. coli LsrF in complex with Ribulose-5-phosphate · 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 P76143
- Elsewhere: RCSB PDB 3GND · PDBe 3GND · UniProt P76143
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