MolNFT v1 · #156981 · protein

Crystal structure of retinal-bound holo Q108K:K40L:T51W domain-swapped dimer of human cellular retinol binding protein 2

6MKV · Retinol-binding protein 2: “Crystal structure of retinal-bound holo Q108K:K40L:T51W domain-swapped dimer of human cellular retinol…”. X-ray diffraction, 1 ligand (RET), 5 pockets (best druggability 0.84). MolNFT v1 #156981 on…

PDB: 6MKV
Type: protein
Length: 532 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Retinol-binding protein 2
UniProt: P50120
Ligands: RET
Pockets: 5 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 11% helix, 59% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Retinol-binding protein 2	protein	133	11% helix, 59% strand	P50120

Ligands and binding sites

RET · Retinal · ligand · 3 copies · chains B, D, A, C
ACT · Acetate ion · additive · 7 copies · chains B, D, C
GOL · Glycerol · additive · 2 copies · chains B, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	338	0.84	0.93	35	empty
2	271	0.84	0.94	32	RET
3	223	0.83	0.96	31	RET
4	255	0.82	0.94	33	RET, ACT
5	758	0.74	0.80	70	ACT

Interfaces

6 interfaces between chains.

B–D · 4048 Å² buried · 83 hydrogen bonds · protein-protein
A–C · 4019 Å² buried · 76 hydrogen bonds · protein-protein
B–C · 523 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 177 Å² buried · 2 hydrogen bonds · protein-protein
C–D · 150 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 3 cofactor (retinal Schiff base).

Compared structures

6MKV · Crystal structure of Retinal-bound holo Q108K:K40L:T51W domain-swapped dimer of human… · the same entry in another collection · chain A against A, TM-score 1.00
P50120 · AlphaFold monomer V2.0 prediction for retinol-binding protein 2 (P50120) · a predicted model of the same protein · chain A against A, TM-score 0.58

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 P50120
Elsewhere: RCSB PDB 6MKV · PDBe 6MKV · UniProt P50120

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