SMTL ID : 6wgi.1

Atomic model of the mutant OCCM (ORC-Cdc6-Cdt1-Mcm2-7 with Mcm6 WHD truncation) loaded on DNA at 10.5 A resolution

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

4 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.1: 16 residues within 4Å: Chain C: T.82, P.109, P.110, G.111, T.112, G.113, K.114, T.115, A.116, E.224, Y.291, I.299, D.330, K.333 Chain D: S.615, R.616 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:G.111, C:T.112, C:G.113, C:K.114, C:T.115, C:T.115, C:T.115, C:A.116, D:S.615 Salt bridges: C:K.333 AGS.2: 16 residues within 4Å: Chain D: S.432, L.449, P.481, G.482, V.483, G.484, K.485, T.486, L.487, E.567, Y.627, I.635, R.639, A.703, R.704 Chain H: R.267 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:G.482, D:V.483, D:G.484, D:K.485, D:T.486, D:T.486, D:L.487, D:E.567, D:E.567, D:Y.627, D:R.639, D:R.704, D:R.704 Salt bridges: D:K.485, D:R.704, D:R.704 AGS.4: 15 residues within 4Å: Chain G: A.9, F.10, Y.38, S.39, G.40, T.41, G.42, K.43, T.44, Y.45, Y.192, I.200, I.255, F.256 Ligands: MG.5 14 PLIP interactions: 14 interactions with chain G Hydrogen bonds: G:A.9, G:F.10, G:G.40, G:T.41, G:G.42, G:K.43, G:T.44, G:T.44, G:Y.45, G:Y.45, G:Y.192 Salt bridges: G:K.43 pi-Stacking: G:Y.45, G:Y.45 AGS.6: 15 residues within 4Å: Chain G: K.151, K.158 Chain H: Y.61, G.62, R.104, Q.105, S.106, Y.107, K.108, T.109, Y.110, D.217, E.218, P.335, K.338 16 PLIP interactions: 13 interactions with chain H, 3 interactions with chain G Hydrogen bonds: H:Q.105, H:S.106, H:Y.107, H:K.108, H:K.108, H:T.109, H:T.109, H:T.109, H:Y.110, H:K.338, H:K.338, G:K.151, G:K.151, G:K.151 Salt bridges: H:K.108, H:K.108

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain D: L.564, L.565, D.566, I.596, V.598 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:L.565, D:D.566 MG.5: 2 residues within 4Å: Chain G: T.44 Ligands: AGS.4 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:T.44

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yuan, Z. et al., Structural mechanism of helicase loading onto replication origin DNA by ORC-Cdc6. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2020-07-15

Peptides

Cell division control protein 6: C
Origin recognition complex subunit 1: D
Origin recognition complex subunit 2: E
Origin recognition complex subunit 3: F
Origin recognition complex subunit 5: G
Origin recognition complex subunit 4: H
Origin recognition complex subunit 6: I
DNA replication licensing factor MCM2: J
DNA replication licensing factor MCM3: K
DNA replication licensing factor MCM4: L
Minichromosome maintenance protein 5: M
Cell division cycle protein CDT1: N
DNA replication licensing factor MCM6: O
DNA replication licensing factor MCM7: P

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
9

D
A

E
B

F
C

G
E

H
D

I
F

J
2

K
3

L
4

M
5

N
L

O
6

P
7

Cell division control protein 6

Origin recognition complex subunit 1

Origin recognition complex subunit 2

Origin recognition complex subunit 3

Origin recognition complex subunit 5

Origin recognition complex subunit 4

Origin recognition complex subunit 6

DNA replication licensing factor MCM2

DNA replication licensing factor MCM3

DNA replication licensing factor MCM4

Minichromosome maintenance protein 5

Cell division cycle protein CDT1

DNA replication licensing factor MCM6

DNA replication licensing factor MCM7

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