MolNFT v1 · #11124 · protein

Carbamoyl phosphate synthetase from escherichia COLI

1JDB: “Carbamoyl phosphate synthetase from escherichia COLI”. X-ray diffraction, 8 ligands (GLN, ADP, ORN), 20 pockets (best druggability 0.83). MolNFT v1 #11124 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1JDB
Type: protein
Length: 5,748 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Carbamoyl phosphate synthetase
EC: 6.3.5.5
UniProt: P00968, P00907
Ligands: GLN, ADP, ORN, NET, K, MN, CL, PO4
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 4 distinct chains · 36% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, E, H	Carbamoyl phosphate synthetase (EC 6.3.5.5)	protein	1057	40% helix, 20% strand	P00968
C, I, L	Carbamoyl phosphate synthetase (EC 6.3.5.5)	protein	379	24% helix, 31% strand	P00907
F	Carbamoyl phosphate synthetase (EC 6.3.5.5)	protein	380	24% helix, 32% strand	P00907
K	Carbamoyl phosphate synthetase (EC 6.3.5.5)	protein	1060	41% helix, 20% strand	P00968

Ligands and binding sites

GLN · Glutamine · ligand · 8 copies · chains B, C, E, F, H, I, K, L
ADP · Adenosine-5'-diphosphate · ligand · 8 copies · chains B, E, H, K
ORN · L-ornithine · ligand · 4 copies · chains B, E, H, K
NET · Tetraethylammonium ion · ligand · 4 copies · chains B, E, H, K
K · Potassium ion · metal · 29 copies · chains B, C, E, F, H, I, K, L
MN · Manganese (II) ion · metal · 16 copies · chains B, E, H, K
CL · Chloride ion · ion · 29 copies · chains B, C, E, F, H, I, K, L
PO4 · Phosphate ion · ion · 9 copies · chains B, E, H, K

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1064	0.83	0.84	71	CL, ORN, NET
2	1046	0.82	0.83	74	CL, ORN, NET
3	185	0.82	0.97	44	K, PO4, ADP
4	1081	0.82	0.83	75	CL, ORN, NET
5	1188	0.82	0.83	82	CL, ORN, NET

Interfaces

8 interfaces between chains.

B–C · 2471 Å² buried · 47 hydrogen bonds · protein-protein
E–F · 2463 Å² buried · 44 hydrogen bonds · protein-protein
K–L · 2460 Å² buried · 43 hydrogen bonds · protein-protein
H–I · 2451 Å² buried · 44 hydrogen bonds · protein-protein
E–H · 607 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

1JDB · Carbamoyl phosphate synthetase from escherichia COLI · the same entry in another collection · chain E against E, TM-score 1.00
P00968 · AlphaFold monomer V2.0 prediction for carbamoyl-phosphate synthase large chain (P00968) · a predicted model of the same protein · chain H against A, 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 P00968
Every structure of UniProt P00907
Elsewhere: RCSB PDB 1JDB · PDBe 1JDB · UniProt P00968 · UniProt P00907

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