SMTL ID : 4r7z.1

PfMCM-AAA double-octamer

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.80 Å

Oligo State

homo-16-mer

Ligands

16 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 14 residues within 4Å: Chain A: I.29, Y.30, Y.32, P.69, G.70, V.71, A.72, K.73, S.74, Q.75, V.219, I.223 Chain H: E.298 Ligands: MG.2 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Y.30, A:Y.30, A:G.70, A:V.71, A:A.72, A:K.73, A:S.74, A:S.74, A:Q.75 Salt bridges: A:K.73 ADP.3: 14 residues within 4Å: Chain A: E.298 Chain B: I.29, Y.30, Y.32, P.69, G.70, V.71, A.72, K.73, S.74, Q.75, V.219, I.223 Ligands: MG.4 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.30, B:Y.30, B:G.70, B:V.71, B:A.72, B:K.73, B:S.74, B:S.74, B:Q.75, A:E.298 Salt bridges: B:K.73 ADP.5: 15 residues within 4Å: Chain B: A.294, E.298 Chain C: I.29, Y.30, Y.32, P.69, G.70, V.71, A.72, K.73, S.74, Q.75, V.219, I.223 Ligands: MG.6 11 PLIP interactions: 10 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:Y.30, C:Y.30, C:G.70, C:V.71, C:A.72, C:K.73, C:S.74, C:S.74, C:Q.75, B:E.298 Salt bridges: C:K.73 ADP.7: 15 residues within 4Å: Chain C: A.294, E.298 Chain D: I.29, Y.30, Y.32, P.69, G.70, V.71, A.72, K.73, S.74, Q.75, V.219, I.223 Ligands: MG.8 12 PLIP interactions: 10 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:Y.30, D:Y.30, D:G.70, D:V.71, D:A.72, D:K.73, D:S.74, D:S.74, D:Q.75, C:E.298, C:E.298 Salt bridges: D:K.73 ADP.9: 14 residues within 4Å: Chain D: E.298 Chain E: I.29, Y.30, Y.32, P.69, G.70, V.71, A.72, K.73, S.74, Q.75, V.219, I.223 Ligands: MG.10 11 PLIP interactions: 1 interactions with chain D, 10 interactions with chain E Hydrogen bonds: D:E.298, E:Y.30, E:Y.30, E:G.70, E:V.71, E:A.72, E:K.73, E:S.74, E:S.74, E:Q.75 Salt bridges: E:K.73 ADP.11: 14 residues within 4Å: Chain E: E.298 Chain F: I.29, Y.30, Y.32, P.69, G.70, V.71, A.72, K.73, S.74, Q.75, V.219, I.223 Ligands: MG.12 11 PLIP interactions: 10 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:Y.30, F:Y.30, F:G.70, F:V.71, F:A.72, F:K.73, F:S.74, F:S.74, F:Q.75, E:E.298 Salt bridges: F:K.73 ADP.13: 15 residues within 4Å: Chain F: A.294, E.298 Chain G: I.29, Y.30, Y.32, P.69, G.70, V.71, A.72, K.73, S.74, Q.75, V.219, I.223 Ligands: MG.14 11 PLIP interactions: 10 interactions with chain G, 1 interactions with chain F Hydrogen bonds: G:Y.30, G:Y.30, G:G.70, G:V.71, G:A.72, G:K.73, G:S.74, G:S.74, G:Q.75, F:E.298 Salt bridges: G:K.73 ADP.15: 14 residues within 4Å: Chain G: E.298 Chain H: I.29, Y.30, Y.32, P.69, G.70, V.71, A.72, K.73, S.74, Q.75, V.219, I.223 Ligands: MG.16 10 PLIP interactions: 10 interactions with chain H Hydrogen bonds: H:Y.30, H:Y.30, H:G.70, H:V.71, H:A.72, H:K.73, H:S.74, H:S.74, H:Q.75 Salt bridges: H:K.73 ADP.17: 15 residues within 4Å: Chain I: I.29, Y.30, Y.32, P.69, G.70, V.71, A.72, K.73, S.74, Q.75, V.219, I.223 Chain P: A.294, E.298 Ligands: MG.18 11 PLIP interactions: 10 interactions with chain I, 1 interactions with chain P Hydrogen bonds: I:Y.30, I:Y.30, I:G.70, I:V.71, I:A.72, I:K.73, I:S.74, I:S.74, I:Q.75, P:E.298 Salt bridges: I:K.73 ADP.19: 15 residues within 4Å: Chain I: A.294, E.298 Chain J: I.29, Y.30, Y.32, P.69, G.70, V.71, A.72, K.73, S.74, Q.75, V.219, I.223 Ligands: MG.20 11 PLIP interactions: 10 interactions with chain J, 1 interactions with chain I Hydrogen bonds: J:Y.30, J:Y.30, J:G.70, J:V.71, J:A.72, J:K.73, J:S.74, J:S.74, J:Q.75, I:E.298 Salt bridges: J:K.73 ADP.21: 15 residues within 4Å: Chain J: A.294, E.298 Chain K: I.29, Y.30, Y.32, P.69, G.70, V.71, A.72, K.73, S.74, Q.75, V.219, I.223 Ligands: MG.22 11 PLIP interactions: 10 interactions with chain K, 1 interactions with chain J Hydrogen bonds: K:Y.30, K:Y.30, K:G.70, K:V.71, K:A.72, K:K.73, K:S.74, K:S.74, K:Q.75, J:E.298 Salt bridges: K:K.73 ADP.23: 14 residues within 4Å: Chain K: E.298 Chain L: I.29, Y.30, Y.32, P.69, G.70, V.71, A.72, K.73, S.74, Q.75, V.219, I.223 Ligands: MG.24 11 PLIP interactions: 10 interactions with chain L, 1 interactions with chain K Hydrogen bonds: L:Y.30, L:Y.30, L:G.70, L:V.71, L:A.72, L:K.73, L:S.74, L:S.74, L:Q.75, K:E.298 Salt bridges: L:K.73 ADP.25: 14 residues within 4Å: Chain L: E.298 Chain M: I.29, Y.30, Y.32, P.69, G.70, V.71, A.72, K.73, S.74, Q.75, V.219, I.223 Ligands: MG.26 11 PLIP interactions: 10 interactions with chain M, 1 interactions with chain L Hydrogen bonds: M:Y.30, M:Y.30, M:G.70, M:V.71, M:A.72, M:K.73, M:S.74, M:S.74, M:Q.75, L:E.298 Salt bridges: M:K.73 ADP.27: 15 residues within 4Å: Chain M: A.294, E.298 Chain N: I.29, Y.30, Y.32, P.69, G.70, V.71, A.72, K.73, S.74, Q.75, V.219, I.223 Ligands: MG.28 11 PLIP interactions: 10 interactions with chain N, 1 interactions with chain M Hydrogen bonds: N:Y.30, N:Y.30, N:G.70, N:V.71, N:A.72, N:K.73, N:S.74, N:S.74, N:Q.75, M:E.298 Salt bridges: N:K.73 ADP.29: 14 residues within 4Å: Chain N: E.298 Chain O: I.29, Y.30, Y.32, P.69, G.70, V.71, A.72, K.73, S.74, Q.75, V.219, I.223 Ligands: MG.30 11 PLIP interactions: 1 interactions with chain N, 10 interactions with chain O Hydrogen bonds: N:E.298, O:Y.30, O:Y.30, O:G.70, O:V.71, O:A.72, O:K.73, O:S.74, O:S.74, O:Q.75 Salt bridges: O:K.73 ADP.31: 14 residues within 4Å: Chain O: E.298 Chain P: I.29, Y.30, Y.32, P.69, G.70, V.71, A.72, K.73, S.74, Q.75, V.219, I.223 Ligands: MG.32 10 PLIP interactions: 10 interactions with chain P Hydrogen bonds: P:Y.30, P:Y.30, P:G.70, P:V.71, P:A.72, P:K.73, P:S.74, P:S.74, P:Q.75 Salt bridges: P:K.73

16 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: S.74, D.131, E.132 Ligands: ADP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.74 MG.4: 4 residues within 4Å: Chain B: S.74, D.131, E.132 Ligands: ADP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.74 MG.6: 4 residues within 4Å: Chain C: S.74, D.131, E.132 Ligands: ADP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:S.74 MG.8: 4 residues within 4Å: Chain D: S.74, D.131, E.132 Ligands: ADP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:S.74 MG.10: 4 residues within 4Å: Chain E: S.74, D.131, E.132 Ligands: ADP.9 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:S.74 MG.12: 4 residues within 4Å: Chain F: S.74, D.131, E.132 Ligands: ADP.11 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:S.74 MG.14: 4 residues within 4Å: Chain G: S.74, D.131, E.132 Ligands: ADP.13 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:S.74 MG.16: 4 residues within 4Å: Chain H: S.74, D.131, E.132 Ligands: ADP.15 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:S.74 MG.18: 4 residues within 4Å: Chain I: S.74, D.131, E.132 Ligands: ADP.17 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:S.74 MG.20: 4 residues within 4Å: Chain J: S.74, D.131, E.132 Ligands: ADP.19 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:S.74 MG.22: 4 residues within 4Å: Chain K: S.74, D.131, E.132 Ligands: ADP.21 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:S.74 MG.24: 4 residues within 4Å: Chain L: S.74, D.131, E.132 Ligands: ADP.23 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:S.74 MG.26: 4 residues within 4Å: Chain M: S.74, D.131, E.132 Ligands: ADP.25 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:S.74 MG.28: 4 residues within 4Å: Chain N: S.74, D.131, E.132 Ligands: ADP.27 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:S.74 MG.30: 4 residues within 4Å: Chain O: S.74, D.131, E.132 Ligands: ADP.29 1 PLIP interactions: 1 interactions with chain O Metal complexes: O:S.74 MG.32: 4 residues within 4Å: Chain P: S.74, D.131, E.132 Ligands: ADP.31 1 PLIP interactions: 1 interactions with chain P Metal complexes: P:S.74

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miller, J.M. et al., Analysis of the crystal structure of an active MCM hexamer. Elife (2014)

Release Date

2014-10-08

Peptides

Cell division control protein 21: ABCDEFGHIJKLMNOP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

O
O

P
P

Cell division control protein 21