MolNFT v1 · #30719 · protein

Carboxymethylproline synthase (carb) from pectobacterium carotovora, apo enzyme

2A7K: “Carboxymethylproline synthase (carb) from pectobacterium carotovora, apo enzyme”. X-ray diffraction, 13 pockets (best druggability 0.83). MolNFT v1 #30719 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2A7K
Type: protein
Length: 2,074 residues
Chains: 9
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Carb
UniProt: Q9XB60
Pockets: 13 · best druggability 0.83

Structure

x-ray diffraction · 9 distinct chains · 54% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Carb	protein	229	54% helix, 17% strand	Q9XB60
B	Carb	protein	230	54% helix, 17% strand	Q9XB60
C	Carb	protein	238	55% helix, 17% strand	Q9XB60
D	Carb	protein	228	54% helix, 18% strand	Q9XB60
E	Carb	protein	236	56% helix, 17% strand	Q9XB60
F	Carb	protein	226	53% helix, 17% strand	Q9XB60
G	Carb	protein	228	52% helix, 18% strand	Q9XB60
H	Carb	protein	231	52% helix, 18% strand	Q9XB60
I	Carb	protein	228	53% helix, 18% strand	Q9XB60

Pockets

13 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1145	0.83	0.84	138	empty
2	1097	0.83	0.84	134	empty
3	459	0.81	0.89	73	empty
4	347	0.79	0.89	43	empty
5	221	0.75	0.90	35	empty

Interfaces

13 interfaces between chains.

D–E · 939 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 931 Å² buried · 9 hydrogen bonds · protein-protein
H–I · 920 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 917 Å² buried · 9 hydrogen bonds · protein-protein
G–H · 917 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

2A7K · carboxymethylproline synthase (CarB) from pectobacterium carotovora, apo enzyme · the same entry in another collection · chain I against I, TM-score 1.00
Q9XB60 · AlphaFold monomer V2.0 prediction for carboxymethylproline synthase (Q9XB60) · 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 Q9XB60
Elsewhere: RCSB PDB 2A7K · PDBe 2A7K · UniProt Q9XB60

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