MolNFT v1 · #110392 · protein

Ccp gateless cavity

4XV8 · Cytochrome C peroxidase, mitochondrial: “Ccp gateless cavity”. X-ray diffraction, 2 ligands (HEM, BEN), 2 pockets (best druggability 0.82). MolNFT v1 #110392 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4XV8
Type: protein
Length: 289 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytochrome C peroxidase, mitochondrial
EC: 1.11.1.5
UniProt: P00431
Ligands: HEM, BEN
Pockets: 2 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 51% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cytochrome C peroxidase, mitochondrial (EC 1.11.1.5)	protein	289	51% helix, 6% strand	P00431

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · chains A
BEN · Benzamidine · 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	498	0.82	0.88	57	HEM, BEN
2	82	0.41	0.78	16	empty

Compared structures

4XV8 · CcP gateless cavity · the same entry in another collection · chain A against A, TM-score 1.00
P00431 · AlphaFold monomer V2.0 prediction for cytochrome C peroxidase, mitochondrial (P00431) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P00431
Elsewhere: RCSB PDB 4XV8 · PDBe 4XV8 · UniProt P00431

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