SMTL ID : 1ofi.2 (1 other biounit)

Asymmetric complex between HslV and I-domain deleted HslU (H. influenzae)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

hetero-6-12-mer

Ligands

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

ADP.1: 16 residues within 4Å: Chain A: H.16, I.17, I.18, Q.20, P.58, G.60, V.61, G.62, K.63, T.64, E.65, L.202, I.210, A.259 Ligands: MG.2, PO4.3 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:I.18, A:G.60, A:V.61, A:V.61, A:G.62, A:K.63, A:T.64, A:T.64, A:T.64, A:E.65, A:E.65 Water bridges: A:K.63, A:T.64 Salt bridges: A:K.63 ADP.5: 17 residues within 4Å: Chain B: H.16, I.17, I.18, P.58, T.59, G.60, V.61, G.62, K.63, T.64, E.65, L.202, I.210, A.259, R.260 Ligands: MG.6, PO4.7 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:I.18, B:G.60, B:V.61, B:V.61, B:G.62, B:T.64, B:T.64, B:T.64, B:E.65, B:E.65, B:E.65, B:R.260 Water bridges: B:K.80, B:S.174 Salt bridges: B:K.63 ADP.15: 16 residues within 4Å: Chain G: H.16, I.17, I.18, Q.20, P.58, G.60, V.61, G.62, K.63, T.64, E.65, L.202, I.210, A.259 Ligands: MG.16, PO4.17 14 PLIP interactions: 14 interactions with chain G Hydrogen bonds: G:I.18, G:G.60, G:V.61, G:V.61, G:G.62, G:K.63, G:T.64, G:T.64, G:T.64, G:E.65, G:E.65 Water bridges: G:K.63, G:T.64 Salt bridges: G:K.63 ADP.19: 17 residues within 4Å: Chain H: H.16, I.17, I.18, P.58, T.59, G.60, V.61, G.62, K.63, T.64, E.65, L.202, I.210, A.259, R.260 Ligands: MG.20, PO4.21 15 PLIP interactions: 15 interactions with chain H Hydrogen bonds: H:I.18, H:G.60, H:V.61, H:V.61, H:G.62, H:T.64, H:T.64, H:T.64, H:E.65, H:E.65, H:E.65, H:R.260 Water bridges: H:K.80, H:S.174 Salt bridges: H:K.63 ADP.29: 16 residues within 4Å: Chain M: H.16, I.17, I.18, Q.20, P.58, G.60, V.61, G.62, K.63, T.64, E.65, L.202, I.210, A.259 Ligands: MG.30, PO4.31 14 PLIP interactions: 14 interactions with chain M Hydrogen bonds: M:I.18, M:G.60, M:V.61, M:V.61, M:G.62, M:K.63, M:T.64, M:T.64, M:T.64, M:E.65, M:E.65 Water bridges: M:K.63, M:T.64 Salt bridges: M:K.63 ADP.33: 17 residues within 4Å: Chain N: H.16, I.17, I.18, P.58, T.59, G.60, V.61, G.62, K.63, T.64, E.65, L.202, I.210, A.259, R.260 Ligands: MG.34, PO4.35 15 PLIP interactions: 15 interactions with chain N Hydrogen bonds: N:I.18, N:G.60, N:V.61, N:V.61, N:G.62, N:T.64, N:T.64, N:T.64, N:E.65, N:E.65, N:E.65, N:R.260 Water bridges: N:K.80, N:S.174 Salt bridges: N:K.63

24 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.123 Ligands: ADP.1, PO4.3 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain A: E.124 Chain B: E.188 Ligands: PO4.3 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:E.188, A:E.124, H2O.1, H2O.1, H2O.1 MG.6: 3 residues within 4Å: Chain B: D.123 Ligands: ADP.5, PO4.7 No protein-ligand interaction detected (PLIP) MG.8: 5 residues within 4Å: Chain B: T.59, E.124 Chain M: R.146, E.188 Ligands: PO4.7 5 PLIP interactions: 1 interactions with chain M, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: M:E.188, B:E.124, H2O.1, H2O.1, H2O.2 MG.10: 4 residues within 4Å: Chain C: G.157, C.160, V.161, T.163 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:G.157, C:C.160, C:T.163 MG.12: 4 residues within 4Å: Chain D: G.157, C.160, V.161, T.163 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:G.157, D:C.160, D:T.163 MG.13: 4 residues within 4Å: Chain E: G.157, C.160, T.163, N.164 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:G.157, E:C.160, E:T.163 MG.14: 4 residues within 4Å: Chain F: G.157, C.160, V.161, T.163 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:G.157, F:C.160, F:T.163 MG.16: 3 residues within 4Å: Chain G: D.123 Ligands: ADP.15, PO4.17 No protein-ligand interaction detected (PLIP) MG.18: 3 residues within 4Å: Chain G: E.124 Chain H: E.188 Ligands: PO4.17 5 PLIP interactions: 1 interactions with chain H, 1 interactions with chain G, 3 Ligand-Water interactions Metal complexes: H:E.188, G:E.124, H2O.1, H2O.1, H2O.1 MG.20: 3 residues within 4Å: Chain H: D.123 Ligands: ADP.19, PO4.21 No protein-ligand interaction detected (PLIP) MG.22: 5 residues within 4Å: Chain A: R.146, E.188 Chain H: T.59, E.124 Ligands: PO4.21 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain H, 3 Ligand-Water interactions Metal complexes: A:E.188, H:E.124, H2O.1, H2O.1, H2O.2 MG.24: 4 residues within 4Å: Chain I: G.157, C.160, V.161, T.163 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:G.157, I:C.160, I:T.163 MG.26: 4 residues within 4Å: Chain J: G.157, C.160, V.161, T.163 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:G.157, J:C.160, J:T.163 MG.27: 4 residues within 4Å: Chain K: G.157, C.160, T.163, N.164 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:G.157, K:C.160, K:T.163 MG.28: 4 residues within 4Å: Chain L: G.157, C.160, V.161, T.163 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:G.157, L:C.160, L:T.163 MG.30: 3 residues within 4Å: Chain M: D.123 Ligands: ADP.29, PO4.31 No protein-ligand interaction detected (PLIP) MG.32: 3 residues within 4Å: Chain M: E.124 Chain N: E.188 Ligands: PO4.31 5 PLIP interactions: 1 interactions with chain M, 1 interactions with chain N, 3 Ligand-Water interactions Metal complexes: M:E.124, N:E.188, H2O.2, H2O.2, H2O.2 MG.34: 3 residues within 4Å: Chain N: D.123 Ligands: ADP.33, PO4.35 No protein-ligand interaction detected (PLIP) MG.36: 5 residues within 4Å: Chain G: R.146, E.188 Chain N: T.59, E.124 Ligands: PO4.35 5 PLIP interactions: 1 interactions with chain N, 1 interactions with chain G, 3 Ligand-Water interactions Metal complexes: N:E.124, G:E.188, H2O.1, H2O.2, H2O.2 MG.38: 4 residues within 4Å: Chain O: G.157, C.160, V.161, T.163 3 PLIP interactions: 3 interactions with chain O Metal complexes: O:G.157, O:C.160, O:T.163 MG.40: 4 residues within 4Å: Chain P: G.157, C.160, V.161, T.163 3 PLIP interactions: 3 interactions with chain P Metal complexes: P:G.157, P:C.160, P:T.163 MG.41: 4 residues within 4Å: Chain Q: G.157, C.160, T.163, N.164 3 PLIP interactions: 3 interactions with chain Q Metal complexes: Q:G.157, Q:C.160, Q:T.163 MG.42: 4 residues within 4Å: Chain R: G.157, C.160, V.161, T.163 3 PLIP interactions: 3 interactions with chain R Metal complexes: R:G.157, R:C.160, R:T.163

6 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 9 residues within 4Å: Chain A: P.58, T.59, G.60, K.63, E.124 Chain B: E.188 Ligands: ADP.1, MG.2, MG.4 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:P.58, A:T.59, A:G.60 Water bridges: A:T.59, A:D.123, A:D.123, A:D.123, A:S.174 Salt bridges: A:K.63 PO4.7: 11 residues within 4Å: Chain B: G.57, P.58, T.59, G.60, K.63, D.123, E.124 Chain M: E.188 Ligands: ADP.5, MG.6, MG.8 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.59, B:G.60, B:D.123 Water bridges: B:T.64, B:S.174 Salt bridges: B:K.63 PO4.17: 9 residues within 4Å: Chain G: P.58, T.59, G.60, K.63, E.124 Chain H: E.188 Ligands: ADP.15, MG.16, MG.18 9 PLIP interactions: 9 interactions with chain G Hydrogen bonds: G:P.58, G:T.59, G:G.60 Water bridges: G:T.59, G:D.123, G:D.123, G:D.123, G:S.174 Salt bridges: G:K.63 PO4.21: 11 residues within 4Å: Chain A: E.188 Chain H: G.57, P.58, T.59, G.60, K.63, D.123, E.124 Ligands: ADP.19, MG.20, MG.22 6 PLIP interactions: 6 interactions with chain H Hydrogen bonds: H:T.59, H:G.60, H:D.123 Water bridges: H:T.64, H:S.174 Salt bridges: H:K.63 PO4.31: 9 residues within 4Å: Chain M: P.58, T.59, G.60, K.63, E.124 Chain N: E.188 Ligands: ADP.29, MG.30, MG.32 9 PLIP interactions: 9 interactions with chain M Hydrogen bonds: M:P.58, M:T.59, M:G.60 Water bridges: M:T.59, M:D.123, M:D.123, M:D.123, M:S.174 Salt bridges: M:K.63 PO4.35: 11 residues within 4Å: Chain G: E.188 Chain N: G.57, P.58, T.59, G.60, K.63, D.123, E.124 Ligands: ADP.33, MG.34, MG.36 6 PLIP interactions: 6 interactions with chain N Hydrogen bonds: N:T.59, N:G.60, N:D.123 Water bridges: N:T.64, N:S.174 Salt bridges: N:K.63

6 x LVS: 4-IODO-3-NITROPHENYL ACETYL-LEUCINYL-LEUCINYL-LEUCINYL-VINYLSULFONE(Covalent)

LVS.9: 14 residues within 4Å: Chain C: T.1, Q.19, V.20, S.21, K.33, F.46, A.47, G.48, G.49, T.50, G.124, S.125 Chain J: T.107, I.109 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain J Hydrophobic interactions: C:T.1, J:I.109 Hydrogen bonds: C:S.21, C:S.21, C:G.48, C:T.50 LVS.11: 12 residues within 4Å: Chain C: E.92 Chain D: T.1, Q.19, V.20, S.21, L.22, F.46, A.47, G.48, T.50, G.124, S.125 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:T.1, D:L.22, D:T.50 Hydrogen bonds: D:S.21, D:S.21, D:G.48, D:T.50 LVS.23: 14 residues within 4Å: Chain I: T.1, Q.19, V.20, S.21, K.33, F.46, A.47, G.48, G.49, T.50, G.124, S.125 Chain P: T.107, I.109 6 PLIP interactions: 5 interactions with chain I, 1 interactions with chain P Hydrophobic interactions: I:T.1, P:I.109 Hydrogen bonds: I:S.21, I:S.21, I:G.48, I:T.50 LVS.25: 12 residues within 4Å: Chain I: E.92 Chain J: T.1, Q.19, V.20, S.21, L.22, F.46, A.47, G.48, T.50, G.124, S.125 6 PLIP interactions: 6 interactions with chain J Hydrophobic interactions: J:L.22, J:T.50 Hydrogen bonds: J:S.21, J:S.21, J:G.48, J:T.50 LVS.37: 14 residues within 4Å: Chain D: T.107, I.109 Chain O: T.1, Q.19, V.20, S.21, K.33, F.46, A.47, G.48, G.49, T.50, G.124, S.125 6 PLIP interactions: 5 interactions with chain O, 1 interactions with chain D Hydrophobic interactions: O:T.1, D:I.109 Hydrogen bonds: O:S.21, O:S.21, O:G.48, O:T.50 LVS.39: 12 residues within 4Å: Chain O: E.92 Chain P: T.1, Q.19, V.20, S.21, L.22, F.46, A.47, G.48, T.50, G.124, S.125 7 PLIP interactions: 7 interactions with chain P Hydrophobic interactions: P:T.1, P:L.22, P:T.50 Hydrogen bonds: P:S.21, P:S.21, P:G.48, P:T.50

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kwon, A.R. et al., Structure and Reactivity of an Asymmetric Complex between Hslv and I-Domain Deleted Hslu, a Prokaryotic Homolog of the Eukaryotic Proteasome. J.Mol.Biol. (2003)

Release Date

2003-07-03

Peptides

ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU: ABGHMN
ATP-DEPENDENT PROTEASE HSLV: CDEFIJKLOPQR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

G
B

H
C

M
B

N
C

C
H

D
I

E
M

F
N

I
H

J
I

K
M

L
N

O
H

P
I

Q
M

R
N

ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU

ATP-DEPENDENT PROTEASE HSLV

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