MolNFT v1 · #165953 · protein

Structure of the MM7 erbin PDZ variant in complex with a high-affinity peptide

6UBH: “Structure of the MM7 erbin PDZ variant in complex with a high-affinity peptide”. X-ray diffraction, 1 ligand (NA), 5 pockets (best druggability 0.75). MolNFT v1 #165953 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6UBH
Type: protein
Length: 387 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Erbin; Peptide
UniProt: Q96RT1
Ligands: NA
Pockets: 5 · best druggability 0.75

Structure

x-ray diffraction · 3 distinct chains · 11% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Erbin	protein	91	11% helix, 37% strand	Q96RT1
B, C, D	Erbin	protein	92	11% helix, 37% strand	Q96RT1
E, F, G, H	Peptide	protein	5	0% helix, 40% strand	—

Ligands and binding sites

NA · Sodium ion · metal · 3 copies · chains A, C, 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	638	0.75	0.82	58	NA
2	407	0.60	0.76	47	empty
3	143	0.44	0.76	23	empty
4	53	0.34	0.79	19	empty
5	58	0.29	0.75	16	empty

Interfaces

11 interfaces between chains.

D–H · 543 Å² buried · 15 hydrogen bonds · protein-protein
C–G · 503 Å² buried · 15 hydrogen bonds · protein-protein
A–E · 482 Å² buried · 9 hydrogen bonds · protein-protein
B–F · 468 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 450 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

6UBH · Structure of the MM7 Erbin PDZ variant in complex with a high-affinity peptide · the same entry in another collection · chain H against H, TM-score 1.00
Q96RT1 · AlphaFold monomer V2.0 prediction for erbin (Q96RT1) · a predicted model of the same protein · chain A 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 Q96RT1
Elsewhere: RCSB PDB 6UBH · PDBe 6UBH · UniProt Q96RT1

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