MolNFT v1 · #94594 · protein

The crystal structure of an ABC transporter substrate-binding protein from bradyrhizobium japonicum usda 110

4I1D: “The crystal structure of an ABC transporter substrate-binding protein from bradyrhizobium japonicum usda 110”. X-ray diffraction, 2 ligands (MLT, SO4), 11 pockets (best druggability 0.86). MolNFT v1 #94594 on GenesisL1: 3D…

PDB: 4I1D
Type: protein
Length: 1,288 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ABC transporter substrate-binding protein
UniProt: Q89F76
Ligands: MLT, SO4
Pockets: 11 · best druggability 0.86

Structure

x-ray diffraction · 2 distinct chains · 46% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D	ABC transporter substrate-binding protein	protein	322	45% helix, 20% strand	Q89F76
C	ABC transporter substrate-binding protein	protein	322	46% helix, 22% strand	Q89F76

Ligands and binding sites

MLT · D-malate · ligand · 4 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 34 copies · chains A, B, C, D
ACT · Acetate ion · additive · 19 copies · chains A, C, B, D
GOL · Glycerol · additive · 15 copies · chains A, B, D, C

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

Pockets

11 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	1028	0.86	0.87	133	SO4, GOL, MLT, ACT
2	568	0.82	0.87	71	SO4, GOL, ACT, MLT
3	481	0.79	0.86	66	SO4, GOL, ACT, MLT
4	924	0.70	0.75	86	SO4, ACT
5	137	0.46	0.77	27	GOL

Interfaces

5 interfaces between chains.

A–C · 1159 Å² buried · 23 hydrogen bonds · protein-protein
B–D · 1155 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 399 Å² buried · 2 hydrogen bonds · protein-protein
A–D · 43 Å² buried · 1 hydrogen bond · protein-protein
B–C · 42 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 24 modified (engineered).

Compared structures

4I1D · The crystal structure of an ABC transporter substrate-binding protein from Bradyrhizobium… · the same entry in another collection · chain A 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 Q89F76
Elsewhere: RCSB PDB 4I1D · PDBe 4I1D · UniProt Q89F76

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