6GMR: PVHL:EloB:EloC

Name: PDB 6GMR: pVHL:EloB:EloC in complex with (4-(1H-pyrrol-1-yl)phenyl)methanol
Published: 2018-08-08
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

pVHL:EloB:EloC in complex with (4-(1H-pyrrol-1-yl)phenyl)methanol. Determined by X-ray diffraction at 1.75 Å resolution. Released 8 Aug 2018.

Method: X-ray diffraction
Resolution: 1.75 Å
Organism: Homo sapiens
Chains: 4
Atoms: 3,249
Mol. weight: 45.58 kDa
Ligands: F4K
Released: 8 Aug 2018

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

Secondary structure: helices and β-sheets

6GMR contains 20 α-helices and 31 β-strands across 4 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 B: 9 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	1
β-strand	10	1	2
β-strand	12-19	8	1
β-strand	23	1	3
α-helix	24-35	12
α-helix	39-41	3
β-strand	42-46	5	1
β-strand	49-50	2	1
α-helix	51-52	2
β-strand	56	1	3
α-helix	58-60	3
β-strand	68	1	4
β-strand	71	1	4
α-helix	72	1
β-strand	73-79	7	1
β-strand	80-81	2	5
β-strand	84-85	2	5
α-helix	86-88	3
β-strand	90	1	2
α-helix	94-96	3
α-helix	98-100	3
α-helix	101-103	3

Chain C: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	18-22	5	1
β-strand	28-32	5	1
α-helix	33-36	4
α-helix	40-45	6
β-strand	59-61	3	1
α-helix	67-83	17
α-helix	89-92	4
α-helix	97-110	14

Chain H: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	565	1	6
β-strand	572-573	2	6

Chain V: 6 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	71-78	8	6
α-helix	83	1
β-strand	84-89	6	7
β-strand	95-97	3	7
β-strand	101	1	7
β-strand	105-112	8	6
β-strand	116-121	6	7
β-strand	127	1	7
β-strand	129-130	2	6
β-strand	133	1	6
β-strand	136	1	7
β-strand	142	1	8
β-strand	145	1	8
α-helix	146	1
β-strand	147-152	6	6
α-helix	158-169	12
α-helix	172-177	6
α-helix	183-189	7
α-helix	194-207	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Elongin-B	B	protein	118	Homo sapiens	Q15370 (AlphaFold model)
Elongin-C	C	protein	97	Homo sapiens	Q15369 (AlphaFold model)
Hypoxia inducible factor 1alpha, residues 559-577	H	protein	19	Homo sapiens	Q16665 (AlphaFold model)
von Hippel-Lindau disease tumor suppressor	V	protein	163	Homo sapiens	P40337 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>6GMR_1 Elongin-B (chains B)
MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGEC
GFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMKPQDSGSSANEQAVQ

Sequence of entity 2 (C), FASTA

>6GMR_2 Elongin-C (chains C)
MMYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCM
YFTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC

Sequence of entity 3 (H), FASTA

>6GMR_3 Hypoxia inducible factor 1alpha, residues 559-577 (chains H)
DEALAPYIPMDDDFQLRSF

Sequence of entity 4 (V), FASTA

>6GMR_4 von Hippel-Lindau disease tumor suppressor (chains V)
GSHMEAGRPRPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIH
SYRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLV
KPENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIAHQRMGD

Ligands and cofactors

ID	Name	Formula	Copies
F4K	(4-pyrrol-1-ylphenyl)methanol	C11 H11 N O	1

Water and common crystallization additives (SO4, GOL) are not listed.

Primary citation

Surface Probing by Fragment-Based Screening and Computational Methods Identifies Ligandable Pockets on the von Hippel-Lindau (VHL) E3 Ubiquitin Ligase. Lucas, X., Van Molle, I., Ciulli, A. J Med Chem (2018) 61:7387-7393. DOI 10.1021/acs.jmedchem.8b00842 · PubMed

Other PDB entries of the same protein (UniProt Q15370 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7Z76 1.32 Å, Crystal structure of compound 10 in complex with the bromodomain of human SMARCA2 and…
9GIO 1.49 Å, Crystal structure of the VHL-EloC-EloB complex with a covalent compound bound to C77 of…
7JTO 1.7 Å, Crystal structure of Protac MS33 in complex with the WD repeat-containing protein 5 and…
8BDS 1.72 Å, Ternary complex between VCB, BRD4-BD1 and PROTAC 48
4AJY 1.73 Å, von Hippel-Lindau protein-ElonginB-ElonginC complex, bound to Hif1- alpha peptide
6HR2 1.76 Å, Crystal structure of PROTAC 2 in complex with the bromodomain of human SMARCA4 and…
7ZLM 1.79 Å, Crystal structure of SOCS2:ElonginB:ElonginC in complex with compound MN551
6I7Q 1.8 Å, Structure of pVHL-elongin B-elongin C (VCB) in complex with hydroxylated-HIF-2alpha…
8BB3 1.8 Å, Structure of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTAC with PEG linker…
6GFX 1.83 Å, pVHL:EloB:EloC in complex with modified HIF-1a CODD peptide containing…
1LM8 1.85 Å, Structure of a HIF-1a-pVHL-ElonginB-ElonginC Complex
9D1Z 1.88 Å, Structure of G75Q Ubiquitin bound to KLHDC3-EloB/C

Browse structure collections

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