Research workbench
Discovery of glycomimetic ligands via genetically-encoded library of phage displaying mannose-peptides
Analyse Discovery of glycomimetic ligands via genetically-encoded library of phage… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CZS
- Type
- protein
- Length
- 964 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Concanavalin-a; Man-wyd
- UniProt
- P81461
- Ligands
- 8LR, CA, MN
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Concanavalin-a | protein | 237 | 4% helix, 47% strand | P81461 |
| E, F, G, H | Man-wyd | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- 8LR · 2-hydroxyethyl alpha-D-mannopyranoside · ligand · 4 copies · chains A, E, B, F, C, G, D, H
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 726 | 0.83 | 0.87 | 102 | empty |
| 2 | 169 | 0.78 | 0.94 | 35 | empty |
| 3 | 65 | 0.39 | 0.80 | 19 | empty |
| 4 | 50 | 0.32 | 0.77 | 19 | empty |
| 5 | 50 | 0.28 | 0.75 | 20 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1183 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1174 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 1088 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1001 Ų buried · 14 hydrogen bonds · protein-protein
- A–E · 313 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 4 modified (covalent ligand, nonstandard).
Compared structures
- 4CZS · Discovery of Glycomimetic Ligands via Genetically-encoded Library of Phage displaying… · the same entry in another collection · chain H against H, TM-score 1.00
- P81461 · AlphaFold monomer V2.0 prediction for concanavalin-a (P81461) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 P81461
- Elsewhere: RCSB PDB 4CZS · PDBe 4CZS · UniProt P81461
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