MolNFT v1 · #146540 · protein

Human gipr ecd and Fab complex

6DKJ · Fab heavy chain: “Human gipr ecd and Fab complex”. X-ray diffraction, 14 pockets (best druggability 0.68). MolNFT v1 #146540 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6DKJ
Type: protein
Length: 1,077 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab heavy chain; Fab light chain; Gastric inhibitory polypeptide receptor
UniProt: P0DOX5, V9HW34, P48546
Pockets: 14 · best druggability 0.68

Structure

x-ray diffraction · 5 distinct chains · 14% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Fab heavy chain	protein	222	11% helix, 50% strand	P0DOX5
L, B	Fab light chain	protein	213	6% helix, 52% strand	V9HW34
C	Gastric inhibitory polypeptide receptor	protein	102	31% helix, 23% strand	P48546
A	Fab heavy chain	protein	221	10% helix, 51% strand	P0DOX5
D	Gastric inhibitory polypeptide receptor	protein	106	30% helix, 22% strand	P48546

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 2 copies · chains A, B, D

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

Pockets

14 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	293	0.68	0.83	55	empty
2	456	0.60	0.75	55	empty
3	318	0.59	0.77	46	empty
4	201	0.53	0.78	28	empty
5	181	0.50	0.77	27	empty

Interfaces

9 interfaces between chains.

A–B · 1947 Å² buried · 15 hydrogen bonds · protein-protein
H–L · 1939 Å² buried · 16 hydrogen bonds · protein-protein
A–D · 911 Å² buried · 10 hydrogen bonds · protein-protein
H–C · 756 Å² buried · 10 hydrogen bonds · protein-protein
L–A · 422 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 disulfide (disulfide).

Compared structures

6DKJ · human GIPR ECD and Fab complex · the same entry in another collection · chain D against D, TM-score 1.00
P48546 · AlphaFold monomer V2.0 prediction for gastric inhibitory polypeptide receptor (P48546) · a predicted model of the same protein · chain C against A, TM-score 0.93

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 P0DOX5
Every structure of UniProt V9HW34
Every structure of UniProt P48546
Elsewhere: RCSB PDB 6DKJ · PDBe 6DKJ · UniProt P0DOX5 · UniProt V9HW34 · UniProt P48546

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