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Increased distal histidine conformational flexibility in the deoxy form of dehaloperoxidase from amphitrite ornata

Analyse Increased distal histidine conformational flexibility in the deoxy form of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3DR9
Type: protein
Length: 274 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dehaloperoxidase a
UniProt: Q9NAV8
Ligands: HEM, SO4
Pockets: 3 · best druggability 0.70

Structure

x-ray diffraction · 1 distinct chain · 77% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Dehaloperoxidase a	protein	137	77% helix, 1% strand	Q9NAV8

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 3 copies · chains 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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	267	0.70	0.84	28	HEM
2	275	0.69	0.83	28	HEM
3	145	0.41	0.74	27	empty

Interfaces

1 interface between chains.

A–B · 231 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

3DR9 · Increased Distal Histidine Conformational Flexibility in the Deoxy Form of… · 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 Q9NAV8
Elsewhere: RCSB PDB 3DR9 · PDBe 3DR9 · UniProt Q9NAV8

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