PDB entry 6yvt

View 6yvt on RCSB PDB site
Description: HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with MD-253
Class: oxidoreductase
Keywords: oxidoreductase, non-heme dioxygenase, iron, 2-oxoglutarate, hypoxia-inducible factor, hif, hif prolyl hydroxylase domain 2, phd2, egln1, oxygenase, hypoxia, DNA-binding, metal-binding, transcription, helix-loop-helix-beta, dsbh, facial triad, cytoplasm, transcription/epigenetic regulation, signaling, development, cell structure, beta-hydroxylation, transcription activator/inhibitor, ubl conjugation, polymorphism, vitamin c, zinc-finger, familial erythrocytosis, breast cancer, transcription complex
Deposited on 2020-04-28, released 2020-05-20
The last revision prior to the SCOPe 2.08 freeze date was dated 2020-05-20, with a file datestamp of 2020-05-15.
Experiment type: XRAY
Resolution: 2.85 Å
R-factor: N/A
AEROSPACI score: 0.15 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Egl nine homolog 1
    Species: Homo sapiens [TaxId:9606]
    Gene: EGLN1, C1orf12, PNAS-118, PNAS-137
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6yvta_
  • Chain 'B':
    Compound: Egl nine homolog 1
    Species: Homo sapiens [TaxId:9606]
    Gene: EGLN1, C1orf12, PNAS-118, PNAS-137
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6yvtb_
  • Chain 'C':
    Compound: Egl nine homolog 1
    Species: Homo sapiens [TaxId:9606]
    Gene: EGLN1, C1orf12, PNAS-118, PNAS-137
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6yvtc_
  • Chain 'D':
    Compound: Egl nine homolog 1
    Species: Homo sapiens [TaxId:9606]
    Gene: EGLN1, C1orf12, PNAS-118, PNAS-137
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6yvtd_
  • Chain 'E':
    Compound: Egl nine homolog 1
    Species: Homo sapiens [TaxId:9606]
    Gene: EGLN1, C1orf12, PNAS-118, PNAS-137
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6yvte_
  • Chain 'F':
    Compound: Egl nine homolog 1
    Species: Homo sapiens [TaxId:9606]
    Gene: EGLN1, C1orf12, PNAS-118, PNAS-137
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6yvtf_
  • Heterogens: PW2, MN, GOL, SO4, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >6yvtA (A:)
gshmaspngqtkplpalklaleyivpcmnkhgicvvddflgketgqqigdevralhdtgk
ftdgqlvsqksdsskdirgdkitwiegkepgcetigllmssmddlirhcngklgsyking
rtkamvacypgngtgyvrhvdnpngdgrcvtciyylnkdwdakvsggilrifpegkaqfa
diepkfdrllffwsdrrnphevqpayatryaitvwyfdaderarakvkyltgekgvrvel
nkpsdsvgkdvf

    Sequence, based on observed residues (ATOM records): (download) 
    >6yvtA (A:)
lpalklaleyivpcmnkhgicvvddflgketgqqigdevralhdtgdkitwiegkepgce
tigllmssmddlirhcngklgsykingrtkamvacypgngtgyvrhvdnpngdgrcvtci
yylnkdwdakvsggilrifpegkaqfadiepkfdrllffwsdrrnphevqpayatryait
vwyfdaderarakvkyl

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >6yvtB (B:)
gshmaspngqtkplpalklaleyivpcmnkhgicvvddflgketgqqigdevralhdtgk
ftdgqlvsqksdsskdirgdkitwiegkepgcetigllmssmddlirhcngklgsyking
rtkamvacypgngtgyvrhvdnpngdgrcvtciyylnkdwdakvsggilrifpegkaqfa
diepkfdrllffwsdrrnphevqpayatryaitvwyfdaderarakvkyltgekgvrvel
nkpsdsvgkdvf

    Sequence, based on observed residues (ATOM records): (download) 
    >6yvtB (B:)
lpalklaleyivpcmnkhgicvvddflgketgqqigdevralhdtirgdkitwiegkepg
cetigllmssmddlirhcngklgsykingrtkamvacypgngtgyvrhvdnpngdgrcvt
ciyylnkdwdakvsggilrifpegkaqfadiepkfdrllffwsdrrnphevqpayatrya
itvwyfdaderarakvkyl

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >6yvtC (C:)
gshmaspngqtkplpalklaleyivpcmnkhgicvvddflgketgqqigdevralhdtgk
ftdgqlvsqksdsskdirgdkitwiegkepgcetigllmssmddlirhcngklgsyking
rtkamvacypgngtgyvrhvdnpngdgrcvtciyylnkdwdakvsggilrifpegkaqfa
diepkfdrllffwsdrrnphevqpayatryaitvwyfdaderarakvkyltgekgvrvel
nkpsdsvgkdvf

    Sequence, based on observed residues (ATOM records): (download) 
    >6yvtC (C:)
lpalklaleyivpcmnkhgicvvddflgketgqqigdevralhdrgdkitwiegkepgce
tigllmssmddlirhcngklgsykingrtkamvacypgngtgyvrhvdnpngdgrcvtci
yylnkdwdakvsggilrifpegkaqfadiepkfdrllffwsdrrnphevqpayatryait
vwyfdaderarakvky

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >6yvtD (D:)
gshmaspngqtkplpalklaleyivpcmnkhgicvvddflgketgqqigdevralhdtgk
ftdgqlvsqksdsskdirgdkitwiegkepgcetigllmssmddlirhcngklgsyking
rtkamvacypgngtgyvrhvdnpngdgrcvtciyylnkdwdakvsggilrifpegkaqfa
diepkfdrllffwsdrrnphevqpayatryaitvwyfdaderarakvkyltgekgvrvel
nkpsdsvgkdvf

    Sequence, based on observed residues (ATOM records): (download) 
    >6yvtD (D:)
lpalklaleyivpcmnkhgicvvddflgketgqqigdevralhdtdirdkitwiegkepg
cetigllmssmddlirhcngklgsykingrtkamvacypgngtgyvrhvdnpngdgrcvt
ciyylnkdwdakvsggilrifpegkaqfadiepkfdrllffwsdrrnphevqpayatrya
itvwyfdaderarakvkyl

  • Chain 'E':
    Sequence, based on SEQRES records: (download) 
    >6yvtE (E:)
gshmaspngqtkplpalklaleyivpcmnkhgicvvddflgketgqqigdevralhdtgk
ftdgqlvsqksdsskdirgdkitwiegkepgcetigllmssmddlirhcngklgsyking
rtkamvacypgngtgyvrhvdnpngdgrcvtciyylnkdwdakvsggilrifpegkaqfa
diepkfdrllffwsdrrnphevqpayatryaitvwyfdaderarakvkyltgekgvrvel
nkpsdsvgkdvf

    Sequence, based on observed residues (ATOM records): (download) 
    >6yvtE (E:)
lpalklaleyivpcmnkhgicvvddflgketgqqigdevralhdtkitwiegkepgceti
gllmssmddlirhcngklgsykingrtkamvacypgngtgyvrhvdnpngdgrcvtciyy
lnkdwdakvsggilrifpegkaqfadiepkfdrllffwsdrrnphevqpayatryaitvw
yfdaderarakvky

  • Chain 'F':
    Sequence, based on SEQRES records: (download) 
    >6yvtF (F:)
gshmaspngqtkplpalklaleyivpcmnkhgicvvddflgketgqqigdevralhdtgk
ftdgqlvsqksdsskdirgdkitwiegkepgcetigllmssmddlirhcngklgsyking
rtkamvacypgngtgyvrhvdnpngdgrcvtciyylnkdwdakvsggilrifpegkaqfa
diepkfdrllffwsdrrnphevqpayatryaitvwyfdaderarakvkyltgekgvrvel
nkpsdsvgkdvf

    Sequence, based on observed residues (ATOM records): (download) 
    >6yvtF (F:)
lpalklaleyivpcmnkhgicvvddflgketgqqigdevralhdtgdkitwiegkepgce
tigllmssmddlirhcngklgsykingrtkamvacypgngtgyvrhvdnpngdgrcvtci
yylnkdwdakvsggilrifpegkaqfadiepkfdrllffwsdrrnphevqpayatryait
vwyfdaderarakvkyl