6GMN: PVHL:EloB:EloC

pVHL:EloB:EloC in complex with methyl 4H-furo[3,2-b]pyrrole-5-carboxylate. Determined by X-ray diffraction at 1.94 Å resolution. Released 8 Aug 2018.

Method: X-ray diffraction
Resolution: 1.94 Å
Organism: Homo sapiens
Chains: 12
Atoms: 11,441
Mol. weight: 167.37 kDa
Ligands: F4E
Released: 8 Aug 2018

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

Secondary structure: helices and β-sheets

6GMN contains 69 α-helices and 106 β-strands across 12 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: 6 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
β-strand	68	1	4
β-strand	71	1	4
α-helix	72	1
β-strand	73-79	7	1
β-strand	80	1	5
β-strand	85	1	5
α-helix	86-88	3
β-strand	90	1	2
α-helix	91-100	10

Chain B: 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	40-46	7
β-strand	59-61	3	1
α-helix	67-83	17
α-helix	89-94	6
α-helix	97-110	14

Chain C: 5 helices, 11 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	106-112	7	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	147-152	6	6
α-helix	158-169	12
α-helix	172-177	6
α-helix	182-189	8
α-helix	194-198	5

Chain D: 6 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	8
β-strand	10	1	9
β-strand	12-19	8	8
β-strand	23	1	10
α-helix	24-35	12
α-helix	39-41	3
β-strand	42-46	5	8
β-strand	49-50	2	8
α-helix	51-52	2
β-strand	56	1	10
β-strand	68	1	11
β-strand	71	1	11
α-helix	72	1
β-strand	73-79	7	8
α-helix	85-87	3
β-strand	90	1	9
α-helix	91-96	6

Chain E: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	18-22	5	8
β-strand	28-32	5	8
α-helix	33-37	5
α-helix	40-46	7
β-strand	59-61	3	8
α-helix	67-83	17
α-helix	89-94	6
α-helix	97-110	14

Chain F: 7 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	71-78	8	12
α-helix	83	1
β-strand	84-89	6	13
β-strand	95-97	3	13
β-strand	101	1	13
β-strand	106-112	7	12
β-strand	116-121	6	13
β-strand	127	1	13
β-strand	129-130	2	12
β-strand	133	1	12
β-strand	136	1	13
α-helix	142-144	3
α-helix	145-146	2
β-strand	147-152	6	12
α-helix	158-169	12
α-helix	172-177	6
α-helix	182-189	8
α-helix	194-202	9

Chains G and J: 6 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	14
β-strand	10	1	15
β-strand	12-19	8	14
β-strand	23	1	16
α-helix	24-35	12
α-helix	39-41	3
β-strand	42-46	5	14
β-strand	49-50	2	14
α-helix	51-52	2
β-strand	56	1	16
β-strand	68	1	17
β-strand	71	1	17
α-helix	72	1
β-strand	73-79	7	14
β-strand	80-81	2	18
β-strand	84-85	2	18
α-helix	86-88	3
β-strand	90	1	15
α-helix	91-100	10

Chain H: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	18-22	5	14
β-strand	28-32	5	14
α-helix	33-36	4
α-helix	40-46	7
β-strand	59-61	3	14
α-helix	67-83	17
α-helix	89-94	6
α-helix	97-99	3
α-helix	100-110	11

3 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Elongin-B	A	protein	104	Homo sapiens	Q15370 (AlphaFold model)
Elongin-C	B, E, H, K	protein	97	Homo sapiens	Q15369 (AlphaFold model)
von Hippel-Lindau disease tumor suppressor	C, F, L	protein	162	Homo sapiens	P40337 (AlphaFold model)
Elongin-B	D, G, J	protein	104	Homo sapiens	Q15370 (AlphaFold model)
von Hippel-Lindau disease tumor suppressor	I	protein	162	Homo sapiens	P40337 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6GMN_1 Elongin-B (chains A)
MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGEC
GFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMK

Sequence of entity 2 (B, E, H, K), FASTA

>6GMN_2 Elongin-C (chains B, E, H, K)
MMYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCM
YFTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC

Sequence of entity 3 (C, F, L), FASTA

>6GMN_3 von Hippel-Lindau disease tumor suppressor (chains C, F, L)
GSMEAGRPRPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHS
YRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVK
PENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIAHQRMGD

Sequence of entity 4 (D, G, J), FASTA

>6GMN_4 Elongin-B (chains D, G, J)
MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGEC
GFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMK

Sequence of entity 5 (I), FASTA

>6GMN_5 von Hippel-Lindau disease tumor suppressor (chains I)
GSMEAGRPRPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHS
YRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVK
PENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIAHQRMGD

Ligands and cofactors

ID	Name	Formula	Copies
F4E	methyl 4~{H}-furo[3,2-b]pyrrole-5-carboxylate	C8 H7 N O3	2

Water and common crystallization additives (ACT) 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
6GMR 1.75 Å, pVHL:EloB:EloC in complex with (4-(1H-pyrrol-1-yl)phenyl)methanol
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

Browse structure collections

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