MolNFT v1 · #33254 · protein
Structure of a sialic acid binding protein (siap) in the presence of the sialic acid acid analogue NEU5AC2EN
2CEX · Protein HI0146: “Structure of a sialic acid binding protein (siap) in the presence of the sialic acid acid analogue NEU5AC2EN”. X-ray diffraction, 2 ligands (DAN, ZN), 9 pockets (best druggability 0.82). MolNFT v1 #33254 on…
- PDB
- 2CEX
- Type
- protein
- Length
- 1,214 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein HI0146
- UniProt
- P44542
- Ligands
- DAN, ZN
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein HI0146 | protein | 304 | 52% helix, 20% strand | P44542 |
| B | Protein HI0146 | protein | 305 | 52% helix, 21% strand | P44542 |
| C | Protein HI0146 | protein | 300 | 47% helix, 20% strand | P44542 |
| D | Protein HI0146 | protein | 305 | 49% helix, 21% strand | P44542 |
Ligands and binding sites
- DAN · 2-deoxy-2,3-dehydro-N-acetyl-neuraminic acid · ligand · chains B
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D
- GOL · Glycerol · additive · 3 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 836 | 0.82 | 0.85 | 109 | DAN |
| 2 | 1087 | 0.81 | 0.82 | 65 | ZN |
| 3 | 667 | 0.70 | 0.78 | 68 | empty |
| 4 | 626 | 0.65 | 0.75 | 68 | empty |
| 5 | 253 | 0.53 | 0.76 | 43 | empty |
Interfaces
5 interfaces between chains.
- B–C · 590 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 493 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 125 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 41 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 41 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2CEX · Structure of a sialic acid binding protein (SiaP) in the presence of the sialic acid acid… · the same entry in another collection · chain D against D, TM-score 1.00
- P44542 · AlphaFold monomer V2.0 prediction for sialic acid-binding periplasmic protein siap… · a predicted model of the same protein · chain B 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 P44542
- Elsewhere: RCSB PDB 2CEX · PDBe 2CEX · UniProt P44542
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