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Crystal structure of the siroheme decarboxylase nirdl in co- complex with iron-uroporphyrin III analogue

Analyse Crystal structure of the siroheme decarboxylase nirdl in co- complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4CZC
Type: protein
Length: 305 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nird-like protein
UniProt: D3DFS4
Ligands: UFE
Pockets: 2 · best druggability 0.67

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nird-like protein	protein	305	41% helix, 23% strand	D3DFS4

Ligands and binding sites

UFE · Fe(III) Uroporphyrin · ligand · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	634	0.67	0.76	48	empty
2	59	0.35	0.78	14	empty

Modifications

Observed in the structure: 5 modified (engineered).

Compared structures

4CZC · Crystal structure of the siroheme decarboxylase NirDL in co-complex with… · the same entry in another collection · chain A against A, TM-score 1.00
D3DFS4 · AlphaFold monomer V2.0 prediction for siroheme decarboxylase (D3DFS4) · a predicted model of the same protein · chain A against A, TM-score 0.94

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 D3DFS4
Elsewhere: RCSB PDB 4CZC · PDBe 4CZC · UniProt D3DFS4

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