SMTL ID : 5c1b.1

p97-delta709-728 in complex with a UFD1-SHP peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.08 Å

Oligo State

hetero-6-2-mer

Ligands

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

AGS.1: 21 residues within 4Å: Chain A: D.204, I.205, G.206, C.208, P.246, G.247, T.248, G.249, K.250, T.251, L.252, E.304, N.347, I.379, I.382, H.383, G.407, A.408, A.411 Chain B: R.358 Ligands: MG.3 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:G.206, A:G.247, A:T.248, A:T.248, A:T.248, A:G.249, A:K.250, A:K.250, A:T.251, A:T.251, A:L.252, A:N.347, A:H.383 Water bridges: A:T.251, A:D.303 Salt bridges: A:K.250 AGS.2: 23 residues within 4Å: Chain A: D.477, I.478, G.479, L.481, P.519, G.520, C.521, G.522, K.523, T.524, L.525, E.577, N.623, I.655, A.658, N.659, G.683, A.684, T.687 Chain B: R.634, P.635, R.745 Ligands: MG.4 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.479, A:G.479, A:G.520, A:C.521, A:G.522, A:K.523, A:T.524, A:T.524, A:L.525, A:N.623, A:N.623, A:T.687, B:R.745 Salt bridges: A:K.523 AGS.6: 23 residues within 4Å: Chain B: D.204, I.205, G.206, C.208, P.246, G.247, T.248, G.249, K.250, T.251, L.252, E.304, N.347, I.379, I.382, H.383, G.407, A.408, A.411 Chain C: K.235, R.358, F.359 Ligands: MG.8 17 PLIP interactions: 16 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:G.206, B:G.247, B:T.248, B:T.248, B:T.248, B:G.249, B:K.250, B:K.250, B:T.251, B:T.251, B:T.251, B:L.252, B:N.347, B:N.347, B:H.383, C:K.235 Salt bridges: B:K.250 AGS.7: 22 residues within 4Å: Chain B: D.477, I.478, G.479, L.481, P.519, G.520, C.521, G.522, K.523, T.524, L.525, N.623, I.655, A.658, N.659, G.683, A.684, T.687 Chain C: R.634, P.635, R.745 Ligands: MG.9 18 PLIP interactions: 15 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:G.479, B:G.479, B:G.520, B:C.521, B:G.522, B:K.523, B:T.524, B:T.524, B:L.525, B:N.623, B:N.623, B:N.659, C:R.745 Water bridges: B:T.524, B:E.577, C:R.634, C:R.634 Salt bridges: B:K.523 AGS.12: 21 residues within 4Å: Chain C: D.204, I.205, G.206, P.246, G.247, T.248, G.249, K.250, T.251, L.252, E.304, N.347, I.379, I.382, H.383, G.407, A.408, A.411 Chain D: R.358, F.359 Ligands: MG.14 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:G.206, C:G.247, C:T.248, C:T.248, C:T.248, C:G.249, C:K.250, C:K.250, C:T.251, C:T.251, C:T.251, C:L.252, C:N.347 Salt bridges: C:K.250 AGS.13: 22 residues within 4Å: Chain C: D.477, I.478, G.479, L.481, P.519, G.520, C.521, G.522, K.523, T.524, L.525, N.623, I.655, A.658, N.659, G.683, A.684, T.687 Chain D: R.634, P.635, R.745 Ligands: MG.15 17 PLIP interactions: 16 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:G.479, C:G.479, C:G.520, C:C.521, C:G.522, C:K.523, C:T.524, C:T.524, C:T.524, C:L.525, C:N.623, C:N.623, C:T.687, D:R.745 Water bridges: C:T.524, C:E.577 Salt bridges: C:K.523 AGS.17: 22 residues within 4Å: Chain D: D.204, I.205, G.206, C.208, P.246, G.247, T.248, G.249, K.250, T.251, L.252, E.304, N.347, I.379, I.382, H.383, G.407, A.408, A.411 Chain E: R.358, F.359 Ligands: MG.19 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:G.206, D:G.247, D:T.248, D:T.248, D:T.248, D:G.249, D:K.250, D:K.250, D:T.251, D:L.252, D:N.347, D:H.383 Water bridges: D:T.251 Salt bridges: D:K.250 AGS.18: 22 residues within 4Å: Chain D: D.477, I.478, G.479, L.481, P.519, G.520, C.521, G.522, K.523, T.524, L.525, N.623, I.655, A.658, N.659, G.683, A.684, T.687 Chain E: R.634, P.635, R.745 Ligands: MG.20 16 PLIP interactions: 13 interactions with chain D, 3 interactions with chain E Hydrogen bonds: D:G.479, D:G.479, D:G.520, D:C.521, D:G.522, D:K.523, D:T.524, D:T.524, D:L.525, D:N.623, D:N.623, D:T.687, E:R.745 Salt bridges: D:K.523 Water bridges: E:R.634, E:R.634 AGS.21: 22 residues within 4Å: Chain E: D.204, I.205, G.206, C.208, P.246, G.247, T.248, G.249, K.250, T.251, L.252, E.304, N.347, I.379, I.382, H.383, G.407, A.408, A.411 Chain F: R.358, F.359 Ligands: MG.23 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:G.206, E:G.247, E:T.248, E:T.248, E:T.248, E:G.249, E:K.250, E:K.250, E:T.251, E:L.252, E:N.347, E:H.383 Water bridges: E:T.251 Salt bridges: E:K.250 AGS.22: 22 residues within 4Å: Chain E: D.477, I.478, G.479, L.481, P.519, G.520, C.521, G.522, K.523, T.524, L.525, N.623, I.655, A.658, N.659, G.683, A.684, T.687 Chain F: R.634, P.635, R.745 Ligands: MG.24 16 PLIP interactions: 3 interactions with chain F, 13 interactions with chain E Hydrogen bonds: F:R.745, E:G.479, E:G.479, E:G.520, E:C.521, E:G.522, E:K.523, E:T.524, E:T.524, E:L.525, E:N.623 Water bridges: F:R.634, F:R.634, E:T.524, E:E.577 Salt bridges: E:K.523 AGS.26: 22 residues within 4Å: Chain A: R.358, F.359 Chain F: D.204, I.205, G.206, C.208, P.246, G.247, T.248, G.249, K.250, T.251, L.252, E.304, N.347, I.379, I.382, H.383, G.407, A.408, A.411 Ligands: MG.28 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:G.206, F:G.247, F:T.248, F:T.248, F:T.248, F:G.249, F:K.250, F:K.250, F:T.251, F:T.251, F:L.252, F:N.347 Water bridges: F:T.251, F:D.303 Salt bridges: F:K.250 AGS.27: 22 residues within 4Å: Chain A: R.634, P.635, R.745 Chain F: D.477, I.478, G.479, L.481, P.519, G.520, C.521, G.522, K.523, T.524, L.525, N.623, I.655, A.658, N.659, G.683, A.684, T.687 Ligands: MG.29 19 PLIP interactions: 2 interactions with chain A, 17 interactions with chain F Hydrogen bonds: A:R.745, F:G.479, F:G.479, F:G.520, F:C.521, F:G.522, F:K.523, F:T.524, F:T.524, F:L.525, F:N.623, F:N.623, F:N.623, F:T.687 Water bridges: A:R.634, F:T.524, F:T.524, F:T.524 Salt bridges: F:K.523

12 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: T.251, D.303 Ligands: AGS.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.251, H2O.1, H2O.1, H2O.1 MG.4: 3 residues within 4Å: Chain A: T.524, D.576 Ligands: AGS.2 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.524, H2O.1, H2O.1 MG.8: 3 residues within 4Å: Chain B: T.251, D.303 Ligands: AGS.6 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.251, H2O.1, H2O.1, H2O.1 MG.9: 3 residues within 4Å: Chain B: T.524, D.576 Ligands: AGS.7 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.524, H2O.1, H2O.1 MG.14: 3 residues within 4Å: Chain C: T.251, D.303 Ligands: AGS.12 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:T.251, H2O.1, H2O.1, H2O.1 MG.15: 3 residues within 4Å: Chain C: T.524, D.576 Ligands: AGS.13 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:T.524, H2O.1, H2O.1 MG.19: 3 residues within 4Å: Chain D: T.251, D.303 Ligands: AGS.17 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:T.251, H2O.1, H2O.1, H2O.1 MG.20: 3 residues within 4Å: Chain D: T.524, D.576 Ligands: AGS.18 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:T.524, H2O.1, H2O.1 MG.23: 3 residues within 4Å: Chain E: T.251, D.303 Ligands: AGS.21 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:T.251, H2O.1, H2O.1, H2O.1 MG.24: 3 residues within 4Å: Chain E: T.524, D.576 Ligands: AGS.22 3 PLIP interactions: 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:T.524, H2O.1, H2O.1 MG.28: 3 residues within 4Å: Chain F: T.251, D.303 Ligands: AGS.26 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:T.251, H2O.1, H2O.2, H2O.2 MG.29: 3 residues within 4Å: Chain F: T.524, D.576 Ligands: AGS.27 3 PLIP interactions: 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:T.524, H2O.2, H2O.2

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 6 residues within 4Å: Chain A: A.582, R.585, I.600, I.628, D.629, I.632 Ligand excluded by PLIP CL.10: 6 residues within 4Å: Chain B: A.582, R.585, I.600, I.628, D.629, I.632 Ligand excluded by PLIP CL.11: 6 residues within 4Å: Chain C: A.582, R.585, I.600, I.628, D.629, I.632 Ligand excluded by PLIP CL.16: 6 residues within 4Å: Chain D: A.582, R.585, I.600, I.628, D.629, I.632 Ligand excluded by PLIP CL.25: 6 residues within 4Å: Chain E: A.582, R.585, I.600, I.628, D.629, I.632 Ligand excluded by PLIP CL.30: 6 residues within 4Å: Chain F: A.582, R.585, I.600, I.628, D.629, I.632 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.31: 8 residues within 4Å: Chain F: F.681, D.685, E.688, I.689, R.692, A.722, R.723 Ligands: GOL.32 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:R.723 GOL.32: 10 residues within 4Å: Chain A: P.635, D.639, L.641, Q.742, R.745 Chain F: A.684, D.685, E.688, S.725 Ligands: GOL.31 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain F Hydrogen bonds: A:R.745, F:E.688, F:E.688, F:S.725

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hanzelmann, P. et al., Characterization of an Additional Binding Surface on the p97 N-Terminal Domain Involved in Bipartite Cofactor Interactions. Structure (2016)

Release Date

2016-01-13

Peptides

Transitional endoplasmic reticulum ATPase: ABCDEF
Ubiquitin fusion degradation protein 1 homolog: GH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
V

H
U

Transitional endoplasmic reticulum ATPase

Ubiquitin fusion degradation protein 1 homolog

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