6GZY: HOIP-fragment5 complex

Name: PDB 6GZY: HOIP-fragment5 complex
Published: 2019-01-30
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

HOIP-fragment5 complex. Determined by X-ray diffraction at 2.15 Å resolution. Released 30 Jan 2019.

Method: X-ray diffraction
Resolution: 2.15 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,509
Mol. weight: 52.4 kDa
Ligands: FHH, ZN
Released: 30 Jan 2019

Explore 6GZY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6GZY contains 19 α-helices and 18 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 10 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	860-866	7
β-strand	869-870	2	1
β-strand	877-878	2	1
β-strand	887-889	3	2
β-strand	896-898	3	2
β-strand	904	1	2
β-strand	906	1	3
β-strand	923	1	3
α-helix	931-934	4
α-helix	939-948	10
β-strand	972-973	2	4
β-strand	984-985	2	4
α-helix	999-1012	14
α-helix	1017-1020	4
α-helix	1023-1034	12
α-helix	1040-1041	2
α-helix	1046-1060	15
α-helix	1062	1
α-helix	1064	1

Chain B: 9 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	860-865	6
β-strand	868-870	3	5
β-strand	877-879	3	5
β-strand	887-889	3	6
β-strand	896-898	3	6
β-strand	904	1	6
β-strand	905-906	2	7
α-helix	907	1
β-strand	923-924	2	7
α-helix	931-934	4
α-helix	939-948	10
β-strand	972-973	2	8
β-strand	984-985	2	8
α-helix	999-1012	14
α-helix	1017-1020	4
α-helix	1023-1034	12
α-helix	1048-1060	13
α-helix	1062-1064	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase RNF31	A, B	protein	223	Homo sapiens	Q96EP0 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6GZY_1 E3 ubiquitin-protein ligase RNF31 (chains A, B)
GPGPEYQAQGLAMYLQENGIDCPKCKFSYALARGGCMHFHCTQCRHQFCSGCYNAFYAKN
KCPEPNCRVKKSLHGHHPRDCLFYLRDWTALRLQKLLQDNNVMFNTEPPAGARAVPGGGC
RVIEQKEVPNGLRDEACGKETPAGYAGLCQAHYKEYLVSLINAHSLDPATLYEVEELETA
TERYLHVRPQPLAGEDPPAYQARLLQKLTEEVPLGQSIPRRRK

Ligands and cofactors

ID	Name	Formula	Copies
FHH	methyl 4-[(2-oxidanylidene-1,5,6,7-tetrahydrocyclopenta[b]pyridin-3-yl)carbonyl…	C14 H18 N2 O4	2
ZN	Zinc ion	Zn	8

Water and common crystallization additives (SO4, EDO, PGE, NA) are not listed.

Primary citation

Fragment-Based Covalent Ligand Screening Enables Rapid Discovery of Inhibitors for the RBR E3 Ubiquitin Ligase HOIP. Johansson, H., Isabella Tsai, Y.C., Fantom, K. et al. J Am Chem Soc (2019) 141:2703-2712. DOI 10.1021/jacs.8b13193 · PubMed

Other PDB entries of the same protein (UniProt Q96EP0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6KC5 1.54 Å, HOIP-HOIPIN1 complex
4LJO 1.56 Å, Structure of an active ligase (HOIP)/ubiquitin transfer complex
7V8F 1.66 Å, Crystal structure of UBE2L3 bound to HOIP RING1 domain.
4P09 1.7 Å, Crystal structure of HOIP PUB domain
9B0B 1.7 Å, Structure of Optineurin bound to HOIP NZF1 domain
9B12 1.81 Å, Structure of Optineurin bound to HOIP NZF1 domain and M1-linked diubiquitin, crystal…
4OWF 2.0 Å, Crystal structure of the NEMO CoZi in complex with HOIP NZF1 domain
4OYK 2.0 Å, Structure of HOIP PUB domain bound to OTULIN PIM
6SC5 2.1 Å, dAb3/HOIP-RBR-Ligand2
6SC8 2.11 Å, dAb3/HOIP-RBR-Ligand4
6KC6 2.12 Å, HOIP-HOIPIN8 complex
4LJP 2.15 Å, Structure of an active ligase (HOIP-H889A)/ubiquitin transfer complex

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