SMTL ID : 6r3p.2 (1 other biounit)

Crystal structure of human DMC1 ATPase domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-octamer

Ligands

8 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.1: 9 residues within 4Å: Chain A: D.125, A.128, R.173, K.176, I.177, E.180, Y.181 Ligands: PG4.2, P6G.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.125 PEG.5: 1 residues within 4Å: Ligands: P6G.4 No protein-ligand interaction detected (PLIP) PEG.7: 9 residues within 4Å: Chain C: D.125, A.128, R.173, K.176, I.177, E.180, Y.181 Ligands: PG4.8, P6G.9 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.125 PEG.11: 1 residues within 4Å: Ligands: P6G.10 No protein-ligand interaction detected (PLIP) PEG.13: 9 residues within 4Å: Chain E: D.125, A.128, R.173, K.176, I.177, E.180, Y.181 Ligands: PG4.14, P6G.15 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:D.125 PEG.17: 1 residues within 4Å: Ligands: P6G.16 No protein-ligand interaction detected (PLIP) PEG.19: 9 residues within 4Å: Chain G: D.125, A.128, R.173, K.176, I.177, E.180, Y.181 Ligands: PG4.20, P6G.21 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:D.125 PEG.23: 1 residues within 4Å: Ligands: P6G.22 No protein-ligand interaction detected (PLIP)

4 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.2: 8 residues within 4Å: Chain A: S.172, R.173, K.176 Chain H: Y.115, T.116, H.119 Ligands: PEG.1, P6G.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.176 PG4.8: 8 residues within 4Å: Chain C: S.172, R.173, K.176 Chain F: Y.115, T.116, H.119 Ligands: PEG.7, P6G.9 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.176 PG4.14: 8 residues within 4Å: Chain B: Y.115, T.116, H.119 Chain E: S.172, R.173, K.176 Ligands: PEG.13, P6G.15 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:K.176 PG4.20: 8 residues within 4Å: Chain D: Y.115, T.116, H.119 Chain G: S.172, R.173, K.176 Ligands: PEG.19, P6G.21 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:K.176

8 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.3: 8 residues within 4Å: Chain A: D.125, Y.126, A.128, A.129, H.132, Y.181 Ligands: PEG.1, PG4.2 No protein-ligand interaction detected (PLIP) P6G.4: 8 residues within 4Å: Chain B: D.125, Y.126, A.128, A.129, H.132, Y.181 Ligands: PEG.5, 1PE.6 No protein-ligand interaction detected (PLIP) P6G.9: 8 residues within 4Å: Chain C: D.125, Y.126, A.128, A.129, H.132, Y.181 Ligands: PEG.7, PG4.8 No protein-ligand interaction detected (PLIP) P6G.10: 8 residues within 4Å: Chain D: D.125, Y.126, A.128, A.129, H.132, Y.181 Ligands: PEG.11, 1PE.12 No protein-ligand interaction detected (PLIP) P6G.15: 8 residues within 4Å: Chain E: D.125, Y.126, A.128, A.129, H.132, Y.181 Ligands: PEG.13, PG4.14 No protein-ligand interaction detected (PLIP) P6G.16: 8 residues within 4Å: Chain F: D.125, Y.126, A.128, A.129, H.132, Y.181 Ligands: PEG.17, 1PE.18 No protein-ligand interaction detected (PLIP) P6G.21: 8 residues within 4Å: Chain G: D.125, Y.126, A.128, A.129, H.132, Y.181 Ligands: PEG.19, PG4.20 No protein-ligand interaction detected (PLIP) P6G.22: 8 residues within 4Å: Chain H: D.125, Y.126, A.128, A.129, H.132, Y.181 Ligands: PEG.23, 1PE.24 No protein-ligand interaction detected (PLIP)

4 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.6: 7 residues within 4Å: Chain A: Y.115, T.116, H.119 Chain B: S.172, R.173, K.176 Ligands: P6G.4 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.173, B:K.176 1PE.12: 7 residues within 4Å: Chain C: Y.115, T.116, H.119 Chain D: S.172, R.173, K.176 Ligands: P6G.10 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.173, D:K.176 1PE.18: 7 residues within 4Å: Chain E: Y.115, T.116, H.119 Chain F: S.172, R.173, K.176 Ligands: P6G.16 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:R.173, F:K.176 1PE.24: 7 residues within 4Å: Chain G: Y.115, T.116, H.119 Chain H: S.172, R.173, K.176 Ligands: P6G.22 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:R.173, H:K.176

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dunce, J.M. et al., Crystal structure of human DMC1 ATPase domain. To Be Published

Release Date

2019-04-03

Peptides

Meiotic recombination protein DMC1/LIM15 homolog: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
C

D
D

E
C

F
D

G
C

H
D

Meiotic recombination protein DMC1/LIM15 homolog

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