MolNFT v1 · #72573 · protein
Crystal structure of FNCEL5A from F. nodosum RT17-B1
3NCO · Endoglucanase FNCEL5A: “Crystal structure of FNCEL5A from F. nodosum RT17-B1”. X-ray diffraction, 1 ligand (PO4), 3 pockets (best druggability 0.85). MolNFT v1 #72573 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3NCO
- Type
- protein
- Length
- 631 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endoglucanase FNCEL5A; Peptide (ALA)(ASN)(GLU); Peptide (ALA)(ASP)(GLN)
- EC
- 3.2.1.4
- UniProt
- D4PEB3
- Ligands
- PO4
- Pockets
- 3 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endoglucanase FNCEL5A (EC 3.2.1.4) | protein | 313 | 45% helix, 14% strand | D4PEB3 |
| B | Endoglucanase FNCEL5A (EC 3.2.1.4) | protein | 312 | 45% helix, 14% strand | D4PEB3 |
| D | Peptide (ALA)(ASN)(GLU) | protein | 3 | 0% helix, 0% strand | — |
| E | Peptide (ALA)(ASP)(GLN) | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1111 | 0.85 | 0.86 | 101 | empty |
| 2 | 119 | 0.64 | 0.88 | 30 | empty |
| 3 | 74 | 0.34 | 0.76 | 18 | empty |
Interfaces
5 interfaces between chains.
- A–B · 960 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 181 Ų buried · 0 hydrogen bonds · protein-protein
- A–E · 180 Ų buried · 0 hydrogen bonds · protein-protein
- B–E · 178 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 176 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 3NCO · Crystal structure of FnCel5A from F. nodosum Rt17-B1 · 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 D4PEB3
- Elsewhere: RCSB PDB 3NCO · PDBe 3NCO · UniProt D4PEB3
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