SMTL ID : 7jk2.1

Structure of Drosophila ORC bound to poly(dA/dT) DNA and Cdc6 (conformation 1)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

4 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 16 residues within 4Å: Chain C: T.28, L.29, R.30, Y.32, R.61, G.62, S.63, G.64, K.65, T.66, T.67, E.301, K.305 Chain D: R.144, E.147 Ligands: MG.2 13 PLIP interactions: 12 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:R.30, C:R.30, C:R.30, C:G.62, C:K.65, C:T.66, C:T.66, C:T.67, C:T.67 Salt bridges: C:R.61, C:K.65, C:K.65, D:R.144 ATP.3: 17 residues within 4Å: Chain B: K.260 Chain D: L.11, F.12, P.13, R.15, S.43, G.44, T.45, G.46, K.47, T.48, A.49, Q.160, Y.183, I.191, P.245 Ligands: MG.4 11 PLIP interactions: 10 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:P.13, D:G.44, D:T.45, D:G.46, D:K.47, D:T.48, D:A.49 Salt bridges: D:K.47, D:K.47, B:K.260 pi-Stacking: D:F.12 ATP.5: 22 residues within 4Å: Chain C: R.196, R.200 Chain F: V.125, P.129, L.132, P.133, R.135, P.164, G.165, T.166, G.167, K.168, T.169, A.170, E.249, N.282, Y.309, I.317, R.321, A.347, R.348 Ligands: MG.6 16 PLIP interactions: 15 interactions with chain F, 1 interactions with chain C Hydrogen bonds: F:P.133, F:G.165, F:T.166, F:G.167, F:K.168, F:T.169, F:A.170, F:N.282, F:Y.309, F:R.321 Salt bridges: F:K.168, F:K.168, F:R.348, F:R.348, F:R.348, C:R.200 ATP.7: 25 residues within 4Å: Chain F: K.294, R.298 Chain G: S.23, A.24, T.26, L.29, P.30, G.31, R.32, Q.60, P.61, G.62, T.63, G.64, K.65, T.66, A.67, E.139, N.172, Y.200, I.208, R.212, V.241, R.242 Ligands: MG.8 21 PLIP interactions: 20 interactions with chain G, 1 interactions with chain F Hydrogen bonds: G:S.23, G:A.24, G:G.31, G:R.32, G:G.62, G:T.63, G:G.64, G:K.65, G:T.66, G:T.66, G:A.67, G:E.139, G:N.172, G:Y.200, G:Y.200, G:R.212 Salt bridges: G:K.65, G:K.65, G:R.242, G:R.242, F:R.298

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain C: T.66 Chain D: R.144 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.66 MG.4: 3 residues within 4Å: Chain D: T.48, D.126 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.48 MG.6: 3 residues within 4Å: Chain C: R.200 Chain F: T.169 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.169 MG.8: 5 residues within 4Å: Chain F: R.298 Chain G: T.66, D.138, E.139 Ligands: ATP.7 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:T.66

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schmidt, J.M. et al., Structural mechanism for replication origin binding and remodeling by a metazoan origin recognition complex and its co-loader Cdc6. Nat Commun (2020)

Release Date

2020-09-09

Peptides

Origin recognition complex subunit 2: A
Origin recognition complex subunit 3: B
Origin recognition complex subunit 4: C
Origin recognition complex subunit 5: D
Origin recognition complex subunit 6: E
Origin recognition complex subunit 1: F
Cell division control protein: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
D

D
E

E
F

F
A

G
G

Origin recognition complex subunit 2

Origin recognition complex subunit 3

Origin recognition complex subunit 4

Origin recognition complex subunit 5

Origin recognition complex subunit 6

Origin recognition complex subunit 1

Cell division control protein

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