Structure of PHD domain of UHRF1 in complex with H3 peptide
Polymer type: polypeptide(L)
Total | 1H | 13C | 15N | |
---|---|---|---|---|
All | 82.3 % (728 of 885) | 88.0 % (411 of 467) | 74.6 % (252 of 338) | 81.3 % (65 of 80) |
Backbone | 87.2 % (408 of 468) | 96.8 % (152 of 157) | 81.9 % (194 of 237) | 83.8 % (62 of 74) |
Sidechain | 77.9 % (385 of 494) | 83.5 % (259 of 310) | 69.1 % (123 of 178) | 50.0 % (3 of 6) |
Aromatic | 56.0 % (28 of 50) | 64.0 % (16 of 25) | 50.0 % (12 of 24) | 0.0 % (0 of 1) |
Methyl | 88.0 % (44 of 50) | 96.0 % (24 of 25) | 80.0 % (20 of 25) |
1. E3 ubiquitin-protein ligase UHRF1
SGPSCKHCKD DVNRLCRVCA CHLCGGRQDP DKQLMCDECD MAFHIYCLDP PLSSVPSEDE WYCPECRND2. entity 2
ARTKQTARKS TSolvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-100% 13C; U-100% 15N] | 1 mM | |
2 | H20 | natural abundance | 1 mM | |
3 | D2O | natural abundance | 1 mM | |
4 | phosphate | natural abundance | 1 mM | |
5 | NaCl | natural abundance | 1 mM | |
6 | KCl | natural abundance | 1 mM |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | na | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | na | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | na | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | na | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | na | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | na | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | na | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | na | indirect | 0.1013291 |
Varian INOVA - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-100% 13C; U-100% 15N] | 1 mM | |
2 | H20 | natural abundance | 1 mM | |
3 | D2O | natural abundance | 1 mM | |
4 | phosphate | natural abundance | 1 mM | |
5 | NaCl | natural abundance | 1 mM | |
6 | KCl | natural abundance | 1 mM |
Varian INOVA - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-100% 13C; U-100% 15N] | 1 mM | |
2 | H20 | natural abundance | 1 mM | |
3 | D2O | natural abundance | 1 mM | |
4 | phosphate | natural abundance | 1 mM | |
5 | NaCl | natural abundance | 1 mM | |
6 | KCl | natural abundance | 1 mM |
Varian INOVA - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-100% 13C; U-100% 15N] | 1 mM | |
2 | H20 | natural abundance | 1 mM | |
3 | D2O | natural abundance | 1 mM | |
4 | phosphate | natural abundance | 1 mM | |
5 | NaCl | natural abundance | 1 mM | |
6 | KCl | natural abundance | 1 mM |
Varian INOVA - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-100% 13C; U-100% 15N] | 1 mM | |
2 | H20 | natural abundance | 1 mM | |
3 | D2O | natural abundance | 1 mM | |
4 | phosphate | natural abundance | 1 mM | |
5 | NaCl | natural abundance | 1 mM | |
6 | KCl | natural abundance | 1 mM |
Varian INOVA - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-100% 13C; U-100% 15N] | 1 mM | |
2 | H20 | natural abundance | 1 mM | |
3 | D2O | natural abundance | 1 mM | |
4 | phosphate | natural abundance | 1 mM | |
5 | NaCl | natural abundance | 1 mM | |
6 | KCl | natural abundance | 1 mM |
Varian INOVA - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-100% 13C; U-100% 15N] | 1 mM | |
2 | H20 | natural abundance | 1 mM | |
3 | D2O | natural abundance | 1 mM | |
4 | phosphate | natural abundance | 1 mM | |
5 | NaCl | natural abundance | 1 mM | |
6 | KCl | natural abundance | 1 mM |
Varian INOVA - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-100% 13C; U-100% 15N] | 1 mM | |
2 | H20 | natural abundance | 1 mM | |
3 | D2O | natural abundance | 1 mM | |
4 | phosphate | natural abundance | 1 mM | |
5 | NaCl | natural abundance | 1 mM | |
6 | KCl | natural abundance | 1 mM |
Varian INOVA - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-100% 13C; U-100% 15N] | 1 mM | |
2 | H20 | natural abundance | 1 mM | |
3 | D2O | natural abundance | 1 mM | |
4 | phosphate | natural abundance | 1 mM | |
5 | NaCl | natural abundance | 1 mM | |
6 | KCl | natural abundance | 1 mM |
Varian INOVA - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-100% 13C; U-100% 15N] | 1 mM | |
2 | H20 | natural abundance | 1 mM | |
3 | D2O | natural abundance | 1 mM | |
4 | phosphate | natural abundance | 1 mM | |
5 | NaCl | natural abundance | 1 mM | |
6 | KCl | natural abundance | 1 mM |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints | combined_17808_2lgg.nef |
Input source #2: Coordindates | 2lgg.cif |
Diamagnetism of the molecular assembly | True (excluding Oxygen atoms) |
Whether the assembly has a disulfide bond | None |
Whether the assembly has a other bond | True (see coodinates for details) |
Whether the assembly contains a cyclic polymer | None |
Overall data processing status | Warning |
Disulfide bonds
NoneOther bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)
Ptnr_site_1 | Ptnr_site_2 | Redox_state_prediction_1 | Redox_state_prediction_2 | Distance (Ã…) |
---|---|---|---|---|
1:44:HIS:NE2 | 3:2:ZN:ZN | unknown | unknown | n/a |
1:8:CYS:SG | 3:1:ZN:ZN | unknown | unknown | n/a |
1:63:CYS:SG | 3:3:ZN:ZN | unknown | unknown | n/a |
1:16:CYS:SG | 3:1:ZN:ZN | unknown | unknown | n/a |
1:5:CYS:SG | 3:1:ZN:ZN | unknown | unknown | n/a |
1:19:CYS:SG | 3:1:ZN:ZN | unknown | unknown | n/a |
1:21:CYS:SG | 3:2:ZN:ZN | unknown | unknown | n/a |
1:39:CYS:SG | 3:3:ZN:ZN | unknown | unknown | n/a |
1:24:CYS:SG | 3:2:ZN:ZN | unknown | unknown | n/a |
1:66:CYS:SG | 3:3:ZN:ZN | unknown | unknown | n/a |
1:47:CYS:SG | 3:2:ZN:ZN | unknown | unknown | n/a |
1:36:CYS:SG | 3:3:ZN:ZN | unknown | unknown | n/a |
Non-standard residues
Chain_ID | Seq_ID | Comp_ID | Chem_comp_name | Experimental evidences |
---|---|---|---|---|
C | 1 | ZN | ZINC ION | None |
C | 2 | ZN | ZINC ION | None |
C | 3 | ZN | ZINC ION | None |
Sequence alignments
-------320-------330-------340-------350-------360-------370--------- SGPSCKHCKDDVNRLCRVCACHLCGGRQDPDKQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECRND ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| SGPSCKHCKDDVNRLCRVCACHLCGGRQDPDKQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECRND --------10--------20--------30--------40--------50--------60---------
-----390---- ARTKQTARKSTG |||||||||||| ARTKQTARKSTG --------10--
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 69 | 0 | 0 | 100.0 |
B | B | 12 | 0 | 0 | 100.0 |
Content subtype: combined_17808_2lgg.nef
Assigned chemical shifts
-------320-------330-------340-------350-------360-------370--------- SGPSCKHCKDDVNRLCRVCACHLCGGRQDPDKQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECRND ||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||| SGPSCKHCKDDVNRLCRVCACHLCGGRQDPDKQLMCDECDMAFHIYCLD.PLSSVPSEDEWYCPECRND
-----390---- ARTKQTARKSTG ||||||||||| ARTKQTARKST -----390---
Comp_index_ID | Comp_ID | Atom_ID | CS value (ppm) |
---|---|---|---|
332 | HIS | HD1 | 7.371 |
354 | HIS | HD1 | 7.193 |
377 | ARG | HH11 | 9.038 |
377 | ARG | HH12 | 9.038 |
377 | ARG | HH21 | 9.184 |
377 | ARG | HH22 | 9.184 |
377 | ARG | NH2 | 114.331 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 399 | 354 | 88.7 |
13C chemical shifts | 291 | 244 | 83.8 |
15N chemical shifts | 72 | 65 | 90.3 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 135 | 131 | 97.0 |
13C chemical shifts | 138 | 125 | 90.6 |
15N chemical shifts | 63 | 62 | 98.4 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 264 | 223 | 84.5 |
13C chemical shifts | 153 | 119 | 77.8 |
15N chemical shifts | 9 | 3 | 33.3 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 22 | 22 | 100.0 |
13C chemical shifts | 22 | 20 | 90.9 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 25 | 16 | 64.0 |
13C chemical shifts | 24 | 12 | 50.0 |
15N chemical shifts | 1 | 0 | 0.0 |
Comp_index_ID | Comp_ID | Atom_ID | CS value (ppm) |
---|---|---|---|
384 | ARG | HH11 | 7.108 |
384 | ARG | HH12 | 7.108 |
386 | LYS | HZ1 | 9.271 |
386 | LYS | HZ2 | 9.271 |
386 | LYS | HZ3 | 9.271 |
391 | LYS | HZ1 | 9.189 |
391 | LYS | HZ2 | 9.189 |
391 | LYS | HZ3 | 9.189 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 71 | 60 | 84.5 |
13C chemical shifts | 49 | 0 | 0.0 |
15N chemical shifts | 15 | 0 | 0.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 25 | 21 | 84.0 |
13C chemical shifts | 24 | 0 | 0.0 |
15N chemical shifts | 12 | 0 | 0.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 46 | 39 | 84.8 |
13C chemical shifts | 25 | 0 | 0.0 |
15N chemical shifts | 3 | 0 | 0.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 5 | 4 | 80.0 |
13C chemical shifts | 5 | 0 | 0.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|
Covalent bonds
Distance restraints
-------320-------330-------340-------350-------360-------370--------- SGPSCKHCKDDVNRLCRVCACHLCGGRQDPDKQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECRND ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| SGPSCKHCKDDVNRLCRVCACHLCGGRQDPDKQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECRND
-----390---- ARTKQTARKSTG ||||||| |||| ARTKQTA.KSTG
Dihedral angle restraints
-------320-------330-------340-------350-------360-------370--------- SGPSCKHCKDDVNRLCRVCACHLCGGRQDPDKQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECRND ||| ||| ||| ||||||||||||||||||||| ||| ||||||||| ..PSC..CKD...RLC............DPDKQLMCDECDMAFHIYCLD....SVP...EWYCPECRN -------320-------330-------340-------350-------360-------370--------