MolNFT v1 · #120863 · protein

Mntc co-structure with mab 305-78-7

5HDQ · ABC transporter substrate-binding protein: “Mntc co-structure with mab 305-78-7”. X-ray diffraction, 1 ligand (FE), 5 pockets (best druggability 0.63). MolNFT v1 #120863 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5HDQ
Type: protein
Length: 704 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ABC transporter substrate-binding protein; Fab heavy chain; Fab light chain
UniProt: W8TNQ9
Ligands: FE
Pockets: 5 · best druggability 0.63

Structure

x-ray diffraction · 3 distinct chains · 22% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ABC transporter substrate-binding protein	protein	273	46% helix, 14% strand	W8TNQ9
H	Fab heavy chain	protein	213	10% helix, 54% strand	—
L	Fab light chain	protein	218	5% helix, 55% strand	—

Ligands and binding sites

FE · Fe (III) ion · metal · chains A
GOL · Glycerol · additive · chains H, L

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	591	0.63	0.75	61	GOL
2	137	0.40	0.74	23	empty
3	63	0.31	0.75	16	empty
4	56	0.28	0.74	16	empty
5	53	0.28	0.74	14	empty

Interfaces

3 interfaces between chains.

H–L · 1895 Å² buried · 18 hydrogen bonds · protein-protein
A–H · 561 Å² buried · 8 hydrogen bonds · protein-protein
A–L · 248 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5HDQ · MntC co-structure with mAB 305-78-7 · 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 W8TNQ9
Elsewhere: RCSB PDB 5HDQ · PDBe 5HDQ · UniProt W8TNQ9

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