PDB entry 5ydk
View 5ydk on RCSB PDB site
Description: Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, tetrameric form
Class: signaling protein
Keywords: ubiquitin, SIGNALING PROTEIN
Deposited on
2017-09-13, released
2018-03-07
The last revision prior to the SCOPe 2.08 freeze date was dated
2018-03-21, with a file datestamp of
2018-03-16.
Experiment type: XRAY
Resolution: 2.51 Å
R-factor: N/A
AEROSPACI score: 0.22
(click here for full SPACI score report)
Chains and heterogens:
- Chain 'A':
Compound: E3 ubiquitin-protein ligase RNF168
Species: Homo sapiens [TaxId:9606]
Gene: RNF168
Database cross-references and differences (RAF-indexed):
- Chain 'B':
Compound: Ubiquitin-40S ribosomal protein S27a
Species: Homo sapiens [TaxId:9606]
Gene: Rps27a, Uba80, Ubcep1
Database cross-references and differences (RAF-indexed):
Domains in SCOPe 2.08: d5ydkb_ - Chain 'C':
Compound: Ubiquitin-40S ribosomal protein S27a
Species: Homo sapiens [TaxId:9606]
Gene: Rps27a, Uba80, Ubcep1
Database cross-references and differences (RAF-indexed):
Domains in SCOPe 2.08: d5ydkc_ - Chain 'D':
Compound: Ubiquitin-40S ribosomal protein S27a
Species: Homo sapiens [TaxId:9606]
Gene: Rps27a, Uba80, Ubcep1
Database cross-references and differences (RAF-indexed):
Domains in SCOPe 2.08: d5ydkd_ - Chain 'E':
Compound: Ubiquitin-40S ribosomal protein S27a
Species: Homo sapiens [TaxId:9606]
Gene: Rps27a, Uba80, Ubcep1
Database cross-references and differences (RAF-indexed):
Domains in SCOPe 2.08: d5ydke_ - Chain 'F':
Compound: E3 ubiquitin-protein ligase RNF168
Species: Homo sapiens [TaxId:9606]
Gene: RNF168
Database cross-references and differences (RAF-indexed):
- Chain 'G':
Compound: E3 ubiquitin-protein ligase RNF168
Species: Homo sapiens [TaxId:9606]
Gene: RNF168
Database cross-references and differences (RAF-indexed):
- Chain 'H':
Compound: Ubiquitin-40S ribosomal protein S27a
Species: Homo sapiens [TaxId:9606]
Gene: Rps27a, Uba80, Ubcep1
Database cross-references and differences (RAF-indexed):
Domains in SCOPe 2.08: d5ydkh_ - Chain 'I':
Compound: Ubiquitin-40S ribosomal protein S27a
Species: Homo sapiens [TaxId:9606]
Gene: Rps27a, Uba80, Ubcep1
Database cross-references and differences (RAF-indexed):
Domains in SCOPe 2.08: d5ydki_ - Chain 'J':
Compound: Ubiquitin-40S ribosomal protein S27a
Species: Homo sapiens [TaxId:9606]
Gene: Rps27a, Uba80, Ubcep1
Database cross-references and differences (RAF-indexed):
Domains in SCOPe 2.08: d5ydkj_ - Chain 'K':
Compound: Ubiquitin-40S ribosomal protein S27a
Species: Homo sapiens [TaxId:9606]
Gene: Rps27a, Uba80, Ubcep1
Database cross-references and differences (RAF-indexed):
Domains in SCOPe 2.08: d5ydkk_ - Chain 'L':
Compound: E3 ubiquitin-protein ligase RNF168
Species: Homo sapiens [TaxId:9606]
Gene: RNF168
Database cross-references and differences (RAF-indexed):
- Heterogens: GOL, HOH
PDB Chain Sequences:
- Chain 'A':
No sequence available.
- Chain 'B':
Sequence; same for both SEQRES and ATOM records: (download)
>5ydkB (B:)
mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdyn
iqrestlhlvlrlrgg
- Chain 'C':
Sequence, based on SEQRES records: (download)
>5ydkC (C:)
mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdyn
iqkestlhlvlrlrggd
Sequence, based on observed residues (ATOM records): (download)
>5ydkC (C:)
mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdyn
iqkestlhlvlrl
- Chain 'D':
Sequence, based on SEQRES records: (download)
>5ydkD (D:)
mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdyn
iqkestlhlvlrlrggd
Sequence, based on observed residues (ATOM records): (download)
>5ydkD (D:)
mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdyn
iqkestlhlvlrlrg
- Chain 'E':
Sequence; same for both SEQRES and ATOM records: (download)
>5ydkE (E:)
mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdyn
iqrestlhlvlrlrgg
- Chain 'F':
No sequence available.
- Chain 'G':
No sequence available.
- Chain 'H':
Sequence; same for both SEQRES and ATOM records: (download)
>5ydkH (H:)
mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdyn
iqrestlhlvlrlrgg
- Chain 'I':
Sequence, based on SEQRES records: (download)
>5ydkI (I:)
mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdyn
iqkestlhlvlrlrggd
Sequence, based on observed residues (ATOM records): (download)
>5ydkI (I:)
mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdyn
iqkestlhlvlrl
- Chain 'J':
Sequence, based on SEQRES records: (download)
>5ydkJ (J:)
mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdyn
iqkestlhlvlrlrggd
Sequence, based on observed residues (ATOM records): (download)
>5ydkJ (J:)
mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdyn
iqkestlhlvlrl
- Chain 'K':
Sequence; same for both SEQRES and ATOM records: (download)
>5ydkK (K:)
mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdyn
iqrestlhlvlrlrgg
- Chain 'L':
No sequence available.