6WS5: DNA repair protein REV1

Rational drug design of phenazopyridine derivatives as novel inhibitors of Rev1-CT. Determined by X-ray diffraction at 2.47 Å resolution. Released 23 Dec 2020.

Method: X-ray diffraction
Resolution: 2.47 Å
Organism: Homo sapiens
Chains: 3
Atoms: 2,565
Mol. weight: 42.99 kDa
Ligands: U8M
Released: 23 Dec 2020

Explore 6WS5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6WS5 contains 16 α-helices and 13 β-strands across 3 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 CCC: 10 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	15-33	19
α-helix	39-41	3
β-strand	42-47	6	3
β-strand	50-55	6	3
α-helix	58-76	19
β-strand	80-88	9	2
β-strand	94-103	10	2
α-helix	113-115	3
α-helix	116-131	16
α-helix	133-135	3
α-helix	138-141	4
β-strand	145-152	8	2
α-helix	157-163	7
β-strand	171-173	3	2
α-helix	176-178	3
α-helix	184	1
β-strand	185-190	6	2
β-strand	193	1	2
β-strand	198-205	8	2

Chain HHH: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	1159	1	1
β-strand	1162	1	1
α-helix	1165-1178	14
α-helix	1184-1199	16
α-helix	1203-1218	16
α-helix	1223-1243	21
β-strand	1247-1248	2	2

Chain ZZZ: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	1877-1880	4	2
α-helix	1883-1884	2
α-helix	1887-1890	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA repair protein REV1	HHH	protein	95	Homo sapiens	Q9UBZ9 (AlphaFold model)
Mitotic spindle assembly checkpoint protein MAD2B	CCC	protein	227	Homo sapiens	Q9UI95 (AlphaFold model)
DNA polymerase zeta catalytic subunit	ZZZ	protein	52	Homo sapiens	O60673

Sequence of entity 1 (HHH), FASTA

>6WS5_1 DNA repair protein REV1 (chains HHH)
GNLAGAVEFNDVKTLLREWITTISDPMEEDILQVVKYCTDLIEEKDLEKLDLVIKYMKRL
MQQSVESVWNMAFDFILDNVQVVLQQTYGSTLKVT

Sequence of entity 2 (CCC), FASTA

>6WS5_2 Mitotic spindle assembly checkpoint protein MAD2B (chains CCC)
MGSSHHHHHHSQDPNSMTTLTRQDLNFGQVVADVLCEFLEVAVHLILYVREVYPVGIFQK
RKKYNVPVQMSCHPELNQYIQDTLHCVKPLLEKNDVEKVVVVILDKEHRPVEKFVFEITQ
PPLLSISSDSLLSHVEQLLAAFILKISVCDAVLDHNPPGCTFTVLVHTREAATRNMEKIQ
VIKDFPWILADEQDVHMHDPRLIPLKTMTSDILKMQLYVEERAHKGS

Sequence of entity 3 (ZZZ), FASTA

>6WS5_3 DNA polymerase zeta catalytic subunit (chains ZZZ)
MLTPTPDSSPRSTSSPSQSKNGSFTPRTANILKPLMSPPSREEIMATLLDHD

Ligands and cofactors

ID	Name	Formula	Copies
U8M	3-[(Z)-(2,3-difluorophenyl)diazenyl]pyridine-2,6-diamine	C11 H9 F2 N5	1

Primary citation

Structure-Based Drug Design of Phenazopyridine Derivatives as Inhibitors of Rev1 Interactions in Translesion Synthesis. McPherson, K.S., Zaino, A.M., Dash, R.C. et al. ChemMedChem (2021) 16:1126-1132. DOI 10.1002/cmdc.202000893 · PubMed

Other PDB entries of the same protein (UniProt Q9UBZ9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4EXT 1.9 Å, Structure of polymerase-interacting domain of human Rev1 in complex with translesional…
6WS0 2.24 Å, Rational drug design of phenazopyridine derivatives as novel inhibitors of Rev1-CT
6ASR 2.36 Å, REV1 UBM2 domain complex with ubiquitin
3GQC 2.5 Å, Structure of human Rev1-DNA-dNTP ternary complex
4GK0 2.7 Å, Crystal structure of human Rev3-Rev7-Rev1 complex
9VGW 2.7 Å, Crystal structure of human PCNA in complex with REV1 PIP-box
4BA9 2.73 Å, The structural basis for the coordination of Y-family Translesion DNA Polymerases by Rev1
3VU7 2.8 Å, Crystal structure of REV1-REV7-REV3 ternary complex
4GK5 3.21 Å, Crystal structure of human Rev3-Rev7-Rev1-Polkappa complex
2EBW Solution structure of the BRCT domain from human DNA repair protein REV1
2LSI Solution structure of polymerase-interacting domain of human Rev1 in complex with…
2LSK C-terminal domain of human REV1 in complex with DNA-polymerase H (eta)

Browse structure collections

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