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Deletion mutant (delta 141) of molybdopterin synthase

Analyse Deletion mutant (delta 141) of molybdopterin synthase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1NVJ
Type: protein
Length: 740 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Molybdopterin converting factor subunit 2
UniProt: P30749
Ligands: NA
Pockets: 10 · best druggability 0.77

Structure

x-ray diffraction · 6 distinct chains · 34% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Molybdopterin converting factor subunit 2	protein	118	35% helix, 34% strand	P30749
B	Molybdopterin converting factor subunit 2	protein	126	33% helix, 34% strand	P30749
C	Molybdopterin converting factor subunit 2	protein	124	36% helix, 35% strand	P30749
D	Molybdopterin converting factor subunit 2	protein	135	31% helix, 35% strand	P30749
E	Molybdopterin converting factor subunit 2	protein	118	36% helix, 36% strand	P30749
F	Molybdopterin converting factor subunit 2	protein	119	34% helix, 36% strand	P30749

Ligands and binding sites

NA · Sodium ion · metal · 4 copies · chains A, B, C, D, E, F
GOL · Glycerol · additive · 8 copies · chains A, E, B, C, D
FMT · Formic acid · additive · 6 copies · chains A, B, C, D, E, F

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

Pockets

10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	877	0.77	0.80	57	GOL, NA
2	247	0.67	0.84	27	FMT
3	268	0.62	0.80	33	FMT
4	233	0.46	0.73	44	GOL
5	106	0.39	0.75	19	FMT

Interfaces

7 interfaces between chains.

E–F · 1390 Å² buried · 27 hydrogen bonds · protein-protein
C–D · 1329 Å² buried · 27 hydrogen bonds · protein-protein
A–B · 1302 Å² buried · 27 hydrogen bonds · protein-protein
B–C · 514 Å² buried · 14 hydrogen bonds · protein-protein
B–F · 302 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

1NVJ · Deletion Mutant (Delta 141) of Molybdopterin Synthase · the same entry in another collection · chain F against F, TM-score 1.00
P30749 · AlphaFold monomer V2.0 prediction for molybdopterin synthase catalytic subunit (P30749) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P30749
Elsewhere: RCSB PDB 1NVJ · PDBe 1NVJ · UniProt P30749

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