MolNFT v1 · #18833 · protein

Carbapenam synthetase

1Q19 · Cara: “Carbapenam synthetase”. X-ray diffraction, 3 ligands (APC, SSC, MG), 20 pockets (best druggability 0.82). MolNFT v1 #18833 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1Q19
Type: protein
Length: 2,000 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cara
UniProt: Q9XB61
Ligands: APC, SSC, MG
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Cara	protein	500	43% helix, 20% strand	Q9XB61

Ligands and binding sites

APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · 4 copies · chains A, B, C, D
SSC · (2S,5S)-5-carboxymethylproline · ligand · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · 4 copies · chains A, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1095	0.82	0.83	67	empty
2	1060	0.81	0.82	61	empty
3	458	0.80	0.88	54	MG, APC, SSC
4	456	0.80	0.87	49	MG, APC, SSC
5	1171	0.80	0.81	149	empty

Interfaces

6 interfaces between chains.

B–C · 1427 Å² buried · 17 hydrogen bonds · protein-protein
A–D · 1420 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 1221 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 1157 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 137 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

1Q19 · Carbapenam Synthetase · the same entry in another collection · chain D against D, TM-score 1.00
Q9XB61 · AlphaFold monomer V2.0 prediction for carbapenam-3-carboxylate synthase (Q9XB61) · a predicted model of the same protein · chain C against A, TM-score 0.99

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 Q9XB61
Elsewhere: RCSB PDB 1Q19 · PDBe 1Q19 · UniProt Q9XB61

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