MolNFT v1 · #74970 · protein

Protocatechuate 3,4-dioxygenase Y447H mutant

3PCD: “Protocatechuate 3,4-dioxygenase Y447H mutant”. X-ray diffraction, 2 ligands (FE, CO3), 20 pockets (best druggability 0.81). MolNFT v1 #74970 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3PCD
Type: protein
Length: 2,598 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protocatechuate 3,4-dioxygenase
EC: 1.13.11.3
UniProt: P00436, P00437
Ligands: FE, CO3
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 10% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Protocatechuate 3,4-dioxygenase (EC 1.13.11.3)	protein	200	11% helix, 32% strand	P00436
M, N, O, P, Q, R	Protocatechuate 3,4-dioxygenase (EC 1.13.11.3)	protein	233	9% helix, 30% strand	P00437

Ligands and binding sites

FE · Fe (III) ion · metal · 6 copies · chains M, N, O, P, Q, R
CO3 · Carbonate ion · ion · 6 copies · chains A, M, B, N, C, O, D, P, E, Q, F, R
BME · Beta-mercaptoethanol · additive · 6 copies · chains M, N, O, P, Q, R

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

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	776	0.81	0.85	80	empty
2	946	0.81	0.83	100	empty
3	745	0.79	0.83	72	CO3
4	642	0.79	0.84	58	CO3
5	953	0.79	0.81	80	CO3

Interfaces

35 interfaces between chains.

A–M · 3710 Å² buried · 67 hydrogen bonds · protein-protein
E–Q · 3704 Å² buried · 65 hydrogen bonds · protein-protein
C–O · 3695 Å² buried · 62 hydrogen bonds · protein-protein
F–R · 3691 Å² buried · 63 hydrogen bonds · protein-protein
B–N · 3683 Å² buried · 68 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 covalent (additive adduct).

Compared structures

3PCD · Protocatechuate 3,4-dioxygenase Y447H mutant · the same entry in another collection · chain O against O, 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 P00436
Every structure of UniProt P00437
Elsewhere: RCSB PDB 3PCD · PDBe 3PCD · UniProt P00436 · UniProt P00437

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