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Predicting protein conformational response in prospective ligand discovery

Analyse Predicting protein conformational response in prospective ligand discovery in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4NVN
Type: protein
Length: 289 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytochrome C peroxidase
UniProt: B3LRE1
Ligands: HEM, 2O1, PO4
Pockets: 2 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 51% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Cytochrome C peroxidase	protein	289	51% helix, 7% strand	B3LRE1

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · chains B
2O1 · 2,3-dihydrobenzo[h][1,6]naphthyridin-4(1H)-one · ligand · chains B
PO4 · Phosphate ion · ion · 3 copies · chains B

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	454	0.82	0.90	58	HEM, 2O1, PO4
2	90	0.40	0.77	18	PO4

Compared structures

4NVN · Predicting protein conformational response in prospective ligand discovery · the same entry in another collection · chain B against B, 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 B3LRE1
Elsewhere: RCSB PDB 4NVN · PDBe 4NVN · UniProt B3LRE1

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