MolNFT v1 · #61154 · protein

Glomerella cingulata E600-cutinase complex

3DD5: “Glomerella cingulata E600-cutinase complex”. X-ray diffraction, 1 ligand (DEP), 17 pockets (best druggability 0.77). MolNFT v1 #61154 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3DD5
Type: protein
Length: 1,547 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cutinase
EC: 3.1.1.74
UniProt: P11373
Ligands: DEP
Pockets: 17 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D	Cutinase (EC 3.1.1.74)	protein	194	39% helix, 16% strand	P11373
C, E, F, G, H	Cutinase (EC 3.1.1.74)	protein	193	42% helix, 16% strand	P11373

Ligands and binding sites

DEP · Diethyl phosphonate · ligand · 8 copies · chains A, B, C, D, E, F, G, H

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

Pockets

17 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	1195	0.77	0.79	117	empty
2	846	0.69	0.75	79	empty
3	268	0.60	0.79	29	DEP
4	251	0.59	0.79	25	DEP
5	229	0.57	0.79	27	DEP

Interfaces

13 interfaces between chains.

A–D · 504 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 381 Å² buried · 3 hydrogen bonds · protein-protein
E–H · 356 Å² buried · 5 hydrogen bonds · protein-protein
F–G · 331 Å² buried · 2 hydrogen bonds · protein-protein
A–F · 318 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide, 7 covalent (disulfide, covalent ligand).

Compared structures

3DD5 · Glomerella cingulata E600-cutinase complex · the same entry in another collection · chain H against H, TM-score 1.00
P11373 · AlphaFold monomer V2.0 prediction for cutinase 1 (P11373) · a predicted model of the same protein · chain F 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 P11373
Elsewhere: RCSB PDB 3DD5 · PDBe 3DD5 · UniProt P11373

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