5HDT: Human cohesin regulator Pds5B

Human cohesin regulator Pds5B bound to a Wapl peptide. Determined by X-ray diffraction at 2.71 Å resolution. Released 9 Mar 2016.

Method
X-ray diffraction
Resolution
2.71 Å
Organism
Homo sapiens
Chains
3
Atoms
17,504
Mol. weight
263.38 kDa
Ligands
IHP
Released
9 Mar 2016

Explore 5HDT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5HDT contains 153 α-helices and 4 β-strands across 2 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 A: 77 helices, 2 β-strands

ElementResiduesLengthSheet
α-helix28-4417
α-helix50-6314
α-helix66-694
α-helix74-9118
α-helix100-11314
α-helix114-1185
α-helix125-13814
α-helix140-1467
α-helix150-16415
α-helix171-18616
α-helix193-2008
α-helix201-2033
α-helix205-2106
α-helix212-22413
α-helix226-23712
α-helix238-2425
α-helix252-2543
α-helix255-26511
α-helix267-2704
α-helix274-2807
α-helix286-30116
α-helix307-3104
α-helix312-3198
α-helix320-3234
α-helix327-34317
α-helix345-3506
α-helix352-3587
α-helix364-38017
α-helix382-3843
α-helix387-39610
α-helix402-41615
α-helix417-4215
β-strand42411
β-strand42611
α-helix427-4326
α-helix436-4427
α-helix443-4453
α-helix449-45810
α-helix459-4635
α-helix470-48112
α-helix486-51429
α-helix519-53315
α-helix539-55517
α-helix557-56711
α-helix573-58513
α-helix596-60813
α-helix615-62915
α-helix634-6385
α-helix642-65918
α-helix662-6643
α-helix667-67711
α-helix682-69514
α-helix699-7024
α-helix704-72017
α-helix723-73614
α-helix740-75415
α-helix761-7633
α-helix764-77613
α-helix782-7876
α-helix788-79811
α-helix804-8074
α-helix815-8173
α-helix820-83920
α-helix846-85914
α-helix872-89019
α-helix893-8964
α-helix901-9088
α-helix909-9124
α-helix916-93116
α-helix937-9393
α-helix941-9488
α-helix952-97524
α-helix977-9782
α-helix980-9845
α-helix988-9903
α-helix991-100010
α-helix1011-102818
α-helix1036-104712
α-helix1059-107921
Chain B: 76 helices, 2 β-strands
ElementResiduesLengthSheet
α-helix28-4316
α-helix53-6210
α-helix66-694
α-helix74-8916
α-helix100-11314
α-helix114-1185
α-helix126-13813
α-helix140-1467
α-helix150-16415
α-helix171-18616
α-helix193-2008
α-helix205-2106
α-helix212-22413
α-helix226-23712
α-helix238-2425
α-helix252-2543
α-helix255-26511
α-helix267-2704
α-helix274-2807
α-helix286-30015
α-helix307-3104
α-helix312-3198
α-helix320-3234
α-helix327-34317
α-helix348-3503
α-helix352-3587
α-helix364-38017
α-helix382-3843
α-helix387-3959
α-helix396-3983
α-helix402-41615
α-helix417-4215
α-helix428-4314
α-helix436-4416
α-helix442-4454
α-helix449-45810
α-helix459-4635
α-helix470-48314
α-helix486-51429
α-helix521-53313
α-helix545-55511
α-helix558-56710
α-helix573-58311
α-helix598-60811
α-helix615-62915
α-helix633-6386
α-helix642-65918
α-helix661-6644
α-helix667-67711
α-helix682-69514
α-helix696-6983
α-helix699-7024
α-helix704-72017
α-helix723-73614
α-helix740-75314
α-helix764-77613
α-helix782-7887
α-helix789-79810
α-helix815-8173
α-helix820-83920
α-helix846-85914
α-helix872-88918
α-helix893-8964
α-helix901-9088
α-helix909-9124
α-helix916-93116
α-helix937-94812
α-helix952-97524
α-helix981-9844
α-helix988-9903
α-helix991-100010
α-helix1011-102818
α-helix1036-104813
β-strand1051-105222
α-helix1059-107921
α-helix1086-10872
β-strand1098-109922
α-helix1114-11185

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Sister chromatid cohesion protein PDS5 homolog BA, Bprotein1111Homo sapiensQ9NTI5 (AlphaFold model)
Wings apart-like protein homologEprotein33Homo sapiensQ7Z5K2 (AlphaFold model)
Sequence of entity 1 (A, B), FASTA
>5HDT_1 Sister chromatid cohesion protein PDS5 homolog B (chains A, B)
GAMDPEFGRPMEISDKISKEEMVRRLKMVVKTFMDMDQDSEEEKELYLNLALHLASDFFL
KHPDKDVRLLVACCLADIFRIYAPEAPHTSPDKLKDIFMFITRQLKGLEDTKSPQFNRYF
YLLENIAWVKSYNICFELEDSNEIFTQLYRTLFSVINNGHNQKVHMHMVDLMSSIICEGD
TVSQELLDTVLVNLVPAHKNLNKQAYDLAKALLKRTAQAIEPYITNFFNQVLMLGKTSIS
DLSEHVFDLILELYNIDSHLLLSVLPQLEFKLKSNDNEERLQVVKLLAKMFGAKDSELAS
QNKPLWQCYLGRFNDIHVPIRLECVKFASHCLMNHPDLAKDLTEYLKVRSHDPEEAIRHD
VIVSIVTAAKKDILLVNDHLLNFVRERTLDKRWRVRKEAMMGLAQIYKKYALQSAAGKDA
AKQIAWIKDKLLHIYYQNSIDDRLLVERIFAQYMVPHNLETTERMKCLYYLYATLDLNAV
KALNEMWKCQNLLRHQVKDLLDLIKQPKTDASVKAIFSKVMVITRNLPDPGKAQDFMKKF
TQVLEDDEKIRKQLEVLVSPTCSCKQAEGCVREITKKLGNPKQPTNPFLEMIKFLLERIA
PVHIDTESISALIKQVNKSIDGTADDEDEGVPTDQAIRAGLELLKVLSFTHPISFHSAET
FESLLACLKMDDEKVAEAALQIFKNTGSKIEEDFPHIRSALLPVLHHKSKKGPPRQAKYA
IHCIHAIFSSKETQFAQIFEPLHKSLDPSNLEHLITPLVTIGHIALLAPDQFAAPLKSLV
ATFIVKDLLMNDRLPGKKTTKLWVPDEEVSPETMVKIQAIKMMVRWLLGMKNNHSKSGTS
TLRLLTTILHSDGDLTEQGKISKPDMSRLRLAAGSAIVKLAQEPCYHEIITLEQYQLCAL
AINDECYQVRQVFAQKLHKGLSRLRLPLEYMAICALCAKDPVKERRAHARQCLVKNINVR
REYLKQHAAVSEKLLSLLPEYVVPYTIHLLAHDPDYVKVQDIEQLKDVKECLWFVLEILM
AKNENNSHAFIRKMVENIKQTKDAQGPDDAKMNEKLYTVCDVAMNIIMSKSTTYSLESPK
DPVLPARFFTQPDKNFSNTKNYLPPEMKSFF
Sequence of entity 2 (E), FASTA
>5HDT_2 Wings apart-like protein homolog (chains E)
MTSRFGKTYSRKGGNGSSKFDEVFSNKRTTLST

Ligands and cofactors

IDNameFormulaCopies
IHPInositol hexakisphosphateC6 H18 O24 P62

Primary citation

Structure of the human cohesin regulator Pds5 in complex with Wapl motif. Ouyang, Z., Tomchick, D.R., Yu, H. To be published.

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