MolNFT v1 · #135429 · protein

Crystal structure of the PDZ domain of rhogef bound to CXCR2 C- terminal peptide

5TYT · Rho guanine nucleotide exchange factor 11, C-X-C chemokine…: “Crystal structure of the PDZ domain of rhogef bound to CXCR2 C- terminal peptide”. X-ray diffraction, 1 pocket (best druggability 0.76). MolNFT v1 #135429 on GenesisL1…

PDB: 5TYT
Type: protein
Length: 354 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rho guanine nucleotide exchange factor 11, C-X-C chemokine receptor type 2 chimera
UniProt: O15085, P25025
Pockets: 1 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 15% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D	Rho guanine nucleotide exchange factor 11, C-X-C chemokine receptor type 2 chimera	protein	89	15% helix, 48% strand	O15085, P25025
C	Rho guanine nucleotide exchange factor 11, C-X-C chemokine receptor type 2 chimera	protein	87	15% helix, 43% strand	O15085, P25025

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1073	0.76	0.78	73	empty

Interfaces

5 interfaces between chains.

C–D · 558 Å² buried · 14 hydrogen bonds · protein-protein
A–C · 426 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 422 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 251 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 120 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

5TYT · Crystal Structure of the PDZ domain of RhoGEF bound to CXCR2 C-terminal peptide · the same entry in another collection · chain A against A, TM-score 1.00
O15085 · AlphaFold monomer V2.0 prediction for rho guanine nucleotide exchange factor 11 (O15085) · a predicted model of the same protein · chain C against A, TM-score 0.92
P25025 · AlphaFold monomer V2.0 prediction for C-X-C chemokine receptor type 2 (P25025) · a predicted model of the same protein · chain D against A, TM-score 0.35

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 O15085
Every structure of UniProt P25025
Elsewhere: RCSB PDB 5TYT · PDBe 5TYT · UniProt O15085 · UniProt P25025

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