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Staphylococcus aureus molybdopterin synthase in complex with precursor Z

Analyse Staphylococcus aureus molybdopterin synthase in complex with precursor Z in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2QIE
Type: protein
Length: 847 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Molybdopterin-converting factor subunit 2; Molybdopterin synthase small subunit
UniProt: P65401, Q7A441
Ligands: 8CS
Pockets: 6 · best druggability 0.62

Structure

x-ray diffraction · 3 distinct chains · 31% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, K, E	Molybdopterin-converting factor subunit 2	protein	136	32% helix, 37% strand	P65401
B, G, J, D	Molybdopterin synthase small subunit	protein	77	27% helix, 27% strand	Q7A441
H	Molybdopterin-converting factor subunit 2	protein	131	33% helix, 34% strand	P65401

Ligands and binding sites

8CS · (2r,4ar,5ar,11ar,12as)-8-amino-2-hydroxy-4A,5A,9,11,11A,12A-hexahydro[1,3,2]dioxaphosphinino[4',5':5,6]pyrano[3,2-g]pteridine-10,12(4H,6H)-dione 2-oxide · ligand · 4 copies · chains A, B, E, H, G, K, J, D

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

Pockets

6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	199	0.62	0.83	28	8CS
2	176	0.59	0.82	26	8CS
3	223	0.59	0.80	32	8CS
4	168	0.57	0.81	27	8CS
5	62	0.45	0.83	14	empty

Interfaces

7 interfaces between chains.

H–K · 1645 Å² buried · 30 hydrogen bonds · protein-protein
A–E · 1590 Å² buried · 34 hydrogen bonds · protein-protein
K–J · 999 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 992 Å² buried · 18 hydrogen bonds · protein-protein
E–D · 970 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

2QIE · Staphylococcus aureus molybdopterin synthase in complex with precursor Z · the same entry in another collection · chain D against D, TM-score 1.00
P65401 · AlphaFold monomer V2.0 prediction for molybdopterin synthase catalytic subunit (P65401) · a predicted model of the same protein · chain A against A, TM-score 0.98
Q7A441 · AlphaFold monomer V2.0 prediction for molybdopterin synthase sulfur carrier subunit… · a predicted model of the same protein · chain B 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 P65401
Every structure of UniProt Q7A441
Elsewhere: RCSB PDB 2QIE · PDBe 2QIE · UniProt P65401 · UniProt Q7A441

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