MolNFT v1 · #50239 · protein

Dfp modified degs delta PDZ

2RCE · Protease degs: “Dfp modified degs delta PDZ”. X-ray diffraction, 15 pockets (best druggability 0.70). MolNFT v1 #50239 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2RCE
Type: protein
Length: 1,848 residues
Chains: 9
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protease degs
EC: 3.4.21.-
UniProt: P0AEE3
Pockets: 15 · best druggability 0.70

Structure

x-ray diffraction · 9 distinct chains · 15% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protease degs (EC 3.4.21.-)	protein	205	15% helix, 39% strand	P0AEE3
B	Protease degs (EC 3.4.21.-)	protein	213	15% helix, 39% strand	P0AEE3
C	Protease degs (EC 3.4.21.-)	protein	214	14% helix, 38% strand	P0AEE3
D	Protease degs (EC 3.4.21.-)	protein	207	15% helix, 42% strand	P0AEE3
E	Protease degs (EC 3.4.21.-)	protein	203	15% helix, 42% strand	P0AEE3
F	Protease degs (EC 3.4.21.-)	protein	211	16% helix, 39% strand	P0AEE3
G	Protease degs (EC 3.4.21.-)	protein	205	16% helix, 35% strand	P0AEE3
H	Protease degs (EC 3.4.21.-)	protein	192	16% helix, 38% strand	P0AEE3
I	Protease degs (EC 3.4.21.-)	protein	198	15% helix, 40% strand	P0AEE3

Pockets

15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	55	0.70	0.98	18	empty
2	57	0.69	0.98	19	empty
3	56	0.69	0.98	19	empty
4	823	0.69	0.75	65	empty
5	597	0.62	0.74	70	empty

Interfaces

15 interfaces between chains.

A–B · 1340 Å² buried · 29 hydrogen bonds · protein-protein
G–I · 1317 Å² buried · 28 hydrogen bonds · protein-protein
B–C · 1309 Å² buried · 23 hydrogen bonds · protein-protein
E–F · 1308 Å² buried · 29 hydrogen bonds · protein-protein
G–H · 1278 Å² buried · 27 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 modified (nonstandard).

Compared structures

2RCE · DFP modified DegS delta PDZ · the same entry in another collection · chain I against I, TM-score 1.00
P0AEE3 · AlphaFold monomer V2.0 prediction for serine endoprotease degs (P0AEE3) · a predicted model of the same protein · chain I against A, TM-score 0.98

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 P0AEE3
Elsewhere: RCSB PDB 2RCE · PDBe 2RCE · UniProt P0AEE3

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