MolNFT v1 · #59266 · protein

Crystal structure of the transthyretin-retinol binding protein-Fab complex

3BSZ: “Crystal structure of the transthyretin-retinol binding protein-Fab complex”. X-ray diffraction, 1 ligand (RTL), 20 pockets (best druggability 0.83). MolNFT v1 #59266 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3BSZ
Type: protein
Length: 1,684 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transthyretin; Plasma retinol-binding protein; Fab fragment heavy chain; Fab fragment…
UniProt: P02766, P02753
Ligands: RTL
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 4 distinct chains · 5% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Transthyretin	protein	119	6% helix, 45% strand	P02766
E, F	Plasma retinol-binding protein	protein	174	10% helix, 41% strand	P02753
L, M	Fab fragment heavy chain	protein	215	3% helix, 45% strand	—
H, N	Fab fragment light chain	protein	215	3% helix, 43% strand	—

Ligands and binding sites

RTL · Retinol · ligand · 2 copies · chains B, E, D, F

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

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	213	0.83	0.96	29	RTL
2	201	0.82	0.95	30	RTL
3	850	0.80	0.83	107	empty
4	566	0.70	0.79	53	empty
5	544	0.69	0.79	57	empty

Interfaces

18 interfaces between chains.

L–H · 1566 Å² buried · 14 hydrogen bonds · protein-protein
M–N · 1502 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 932 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 906 Å² buried · 17 hydrogen bonds · protein-protein
E–N · 507 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 disulfide (disulfide).

Compared structures

3BSZ · Crystal structure of the transthyretin-retinol binding protein-Fab complex · the same entry in another collection · chain N against N, TM-score 1.00
P02753 · AlphaFold monomer V2.0 prediction for retinol-binding protein 4 (P02753) · a predicted model of the same protein · chain E 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 P02766
Every structure of UniProt P02753
Elsewhere: RCSB PDB 3BSZ · PDBe 3BSZ · UniProt P02766 · UniProt P02753

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