PDB entry 1ybd
View 1ybd on RCSB PDB site
Description: Crystal structure analysis of uridylate kinase from Neisseria meningitidis
Class: transferase
Keywords: alpha/beta/alpha fold, Kinase, Hexamer, Structural Genomics, Protein Structure Initiative, PSI, New York SGX Research Center for Structural Genomics, NYSGXRC, T1843, TRANSFERASE
Deposited on
2004-12-20, released
2005-02-15
The last revision prior to the SCOPe 2.08 freeze date was dated
2021-02-03, with a file datestamp of
2021-01-29.
Experiment type: XRAY
Resolution: 2.6 Å
R-factor: N/A
AEROSPACI score: 0.27
(click here for full SPACI score report)
Chains and heterogens:
- Chain 'A':
Compound: uridylate kinase
Species: Neisseria meningitidis [TaxId:487]
Gene: pyrH
Database cross-references and differences (RAF-indexed):
- Uniprot P65932 (Start-238)
- modified residue (19)
- modified residue (44)
- modified residue (68)
- modified residue (76)
- modified residue (78-79)
- modified residue (83)
- modified residue (107)
- modified residue (153)
- modified residue (158)
- modified residue (197)
Domains in SCOPe 2.08: d1ybda1 - Chain 'B':
Compound: uridylate kinase
Species: Neisseria meningitidis [TaxId:487]
Gene: pyrH
Database cross-references and differences (RAF-indexed):
- Uniprot P65932 (Start-238)
- modified residue (19)
- modified residue (44)
- modified residue (68)
- modified residue (76)
- modified residue (78-79)
- modified residue (83)
- modified residue (107)
- modified residue (153)
- modified residue (158)
- modified residue (197)
Domains in SCOPe 2.08: d1ybdb_ - Chain 'C':
Compound: uridylate kinase
Species: Neisseria meningitidis [TaxId:487]
Gene: pyrH
Database cross-references and differences (RAF-indexed):
- Uniprot P65932 (Start-238)
- modified residue (19)
- modified residue (44)
- modified residue (68)
- modified residue (76)
- modified residue (78-79)
- modified residue (83)
- modified residue (107)
- modified residue (153)
- modified residue (158)
- modified residue (197)
Domains in SCOPe 2.08: d1ybdc_ - Heterogens: FMT, GOL, HOH
PDB Chain Sequences:
- Chain 'A':
Sequence, based on SEQRES records: (download)
>1ybdA (A:)
mtqqikykrvllklsgeslmgsdpfginhdtivqtvgeiaevvkmgvqvgivvgggnifr
gvsaqagsmdratadymgmmatvmnalalkdafetlgikarvqsalsmqqiaetyarpka
iqyleegkvvifaagtgnpffttdtaaalrgaemncdvmlkatnvdgvytadpkkdpsat
ryetitfdeallknlkvmdatafalcrerklnivvfgiakegslkrvitgedegtlvhc
Sequence, based on observed residues (ATOM records): (download)
>1ybdA (A:)
qikykrvllklsgeslmgsdpfginhdtivqtvgeiaevvkmgvqvgivvgggnifrgvs
aqagsmdratadymgmmatvmnalalkdafetlgikarvqsalsmqqiaetyarpkaiqy
leegkvvifaagtgnpffttdtaaalrgaemncdvmlkatnvdgvytadpkkdpsatrye
titfdeallknlkvmdatafalcrerklnivvfgiakegslkrvitgedegtlvhc
- Chain 'B':
Sequence, based on SEQRES records: (download)
>1ybdB (B:)
mtqqikykrvllklsgeslmgsdpfginhdtivqtvgeiaevvkmgvqvgivvgggnifr
gvsaqagsmdratadymgmmatvmnalalkdafetlgikarvqsalsmqqiaetyarpka
iqyleegkvvifaagtgnpffttdtaaalrgaemncdvmlkatnvdgvytadpkkdpsat
ryetitfdeallknlkvmdatafalcrerklnivvfgiakegslkrvitgedegtlvhc
Sequence, based on observed residues (ATOM records): (download)
>1ybdB (B:)
qikykrvllklsgeslmgsdpfginhdtivqtvgeiaevvkmgvqvgivvgggnifrgvs
aqagsmdratadymgmmatvmnalalkdafetlgikarvqsalsmqqiaetyarpkaiqy
leegkvvifaagtgnpffttdtaaalrgaemncdvmlkatnvdgvytadpkkdpsatrye
titfdeallknlkvmdatafalcrerklnivvfgiakegslkrvitgedegtlvhc
- Chain 'C':
Sequence, based on SEQRES records: (download)
>1ybdC (C:)
mtqqikykrvllklsgeslmgsdpfginhdtivqtvgeiaevvkmgvqvgivvgggnifr
gvsaqagsmdratadymgmmatvmnalalkdafetlgikarvqsalsmqqiaetyarpka
iqyleegkvvifaagtgnpffttdtaaalrgaemncdvmlkatnvdgvytadpkkdpsat
ryetitfdeallknlkvmdatafalcrerklnivvfgiakegslkrvitgedegtlvhc
Sequence, based on observed residues (ATOM records): (download)
>1ybdC (C:)
qikykrvllklsgeslmgsdpfginhdtivqtvgeiaevvkmgvqvgivvgggnifrgvs
aqagsmdratadymgmmatvmnalalkdafetlgikarvqsalsmqqiaetyarpkaiqy
leegkvvifaagtgnpffttdtaaalrgaemncdvmlkatnvdgvytadpkkdpsatrye
titfdeallknlkvmdatafalcrerklnivvfgiakegslkrvitgedegtlvhc