SMTL ID : 6s1m.1

Human polymerase delta holoenzyme Conformer 1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-3-mer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.1012, C.1015, C.1026, C.1029 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.1012, A:C.1015, A:C.1026, A:C.1029

1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.2: 7 residues within 4Å: Chain A: C.1058, C.1061, C.1071, C.1076, I.1078, F.1079, R.1082 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.1058, A:C.1061, A:C.1071, A:C.1076

1 x TTP: THYMIDINE-5'-TRIPHOSPHATE(Non-covalent)

TTP.3: 13 residues within 4Å: Chain A: F.603, S.604, S.605, L.606, Y.607, R.667, K.694, N.698, Y.701, D.757 Chain H: C.25 Chain I: A.13, G.14 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.607 Hydrogen bonds: A:S.605, A:L.606, A:Y.607, A:N.698 Salt bridges: A:R.667, A:K.694, A:K.694, A:K.694

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lancey, C. et al., Structure of the processive human Pol delta holoenzyme. Nat Commun (2020)

Release Date

2019-12-25

Peptides

DNA polymerase delta catalytic subunit: A
DNA polymerase delta subunit 2: B
DNA polymerase delta subunit 3: C
DNA polymerase delta subunit 4: D
Proliferating cell nuclear antigen: EFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

DNA polymerase delta catalytic subunit

DNA polymerase delta subunit 2

DNA polymerase delta subunit 3

DNA polymerase delta subunit 4

Proliferating cell nuclear antigen

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