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

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

hetero-6-12-mer

Ligands

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

ADP.1: 18 residues within 4Å: Chain A: H.16, I.17, I.18, Q.20, P.58, T.59, G.60, V.61, G.62, K.63, T.64, E.65, L.202, I.210, A.259 Chain D: E.153 Ligands: MG.2, PO4.3 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:I.18, A:I.18, A:G.60, A:V.61, A:G.62, A:K.63, A:T.64, A:T.64, A:T.64, A:E.65, A:E.65, D:E.153 Water bridges: A:K.63 Salt bridges: A:K.63 ADP.8: 18 residues within 4Å: Chain D: H.16, I.17, I.18, Q.20, P.58, T.59, G.60, V.61, G.62, K.63, T.64, E.65, L.202, I.210, A.259 Chain J: E.153 Ligands: MG.9, PO4.10 14 PLIP interactions: 13 interactions with chain D, 1 interactions with chain J Hydrogen bonds: D:I.18, D:I.18, D:G.60, D:V.61, D:G.62, D:K.63, D:T.64, D:T.64, D:T.64, D:E.65, D:E.65, J:E.153 Water bridges: D:K.63 Salt bridges: D:K.63 ADP.15: 18 residues within 4Å: Chain A: E.153 Chain G: H.16, I.17, I.18, Q.20, P.58, T.59, 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: 13 interactions with chain G, 1 interactions with chain A Hydrogen bonds: G:I.18, G:I.18, G:G.60, G:V.61, G:G.62, G:K.63, G:T.64, G:T.64, G:T.64, G:E.65, G:E.65, A:E.153 Water bridges: G:K.63 Salt bridges: G:K.63 ADP.22: 18 residues within 4Å: Chain J: H.16, I.17, I.18, Q.20, P.58, T.59, G.60, V.61, G.62, K.63, T.64, E.65, L.202, I.210, A.259 Chain P: E.153 Ligands: MG.23, PO4.24 14 PLIP interactions: 13 interactions with chain J, 1 interactions with chain P Hydrogen bonds: J:I.18, J:I.18, J:G.60, J:V.61, J:G.62, J:K.63, J:T.64, J:T.64, J:T.64, J:E.65, J:E.65, P:E.153 Water bridges: J:K.63 Salt bridges: J:K.63 ADP.29: 18 residues within 4Å: Chain G: E.153 Chain M: H.16, I.17, I.18, Q.20, P.58, T.59, 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: 13 interactions with chain M, 1 interactions with chain G Hydrogen bonds: M:I.18, M:I.18, M:G.60, M:V.61, M:G.62, M:K.63, M:T.64, M:T.64, M:T.64, M:E.65, M:E.65, G:E.153 Water bridges: M:K.63 Salt bridges: M:K.63 ADP.36: 18 residues within 4Å: Chain M: E.153 Chain P: H.16, I.17, I.18, Q.20, P.58, T.59, G.60, V.61, G.62, K.63, T.64, E.65, L.202, I.210, A.259 Ligands: MG.37, PO4.38 14 PLIP interactions: 13 interactions with chain P, 1 interactions with chain M Hydrogen bonds: P:I.18, P:I.18, P:G.60, P:V.61, P:G.62, P:K.63, P:T.64, P:T.64, P:T.64, P:E.65, P:E.65, M:E.153 Water bridges: P:K.63 Salt bridges: P: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: 4 residues within 4Å: Chain A: E.124 Chain D: R.146, E.188 Ligands: PO4.3 5 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: D:E.188, A:E.124, H2O.1, H2O.1, H2O.1 MG.6: 4 residues within 4Å: Chain B: G.157, C.160, V.161, T.163 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:G.157, B:C.160, B:T.163 MG.7: 5 residues within 4Å: Chain C: G.157, C.160, V.161, F.162, T.163 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:G.157, C:C.160, C:T.163 MG.9: 3 residues within 4Å: Chain D: D.123 Ligands: ADP.8, PO4.10 No protein-ligand interaction detected (PLIP) MG.11: 4 residues within 4Å: Chain D: E.124 Chain J: R.146, E.188 Ligands: PO4.10 5 PLIP interactions: 1 interactions with chain J, 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: J:E.188, D:E.124, H2O.1, H2O.1, H2O.1 MG.13: 4 residues within 4Å: Chain E: G.157, C.160, V.161, T.163 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:G.157, E:C.160, E:T.163 MG.14: 5 residues within 4Å: Chain F: G.157, C.160, V.161, F.162, 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: 4 residues within 4Å: Chain A: R.146, E.188 Chain G: E.124 Ligands: PO4.17 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain G, 3 Ligand-Water interactions Metal complexes: A:E.188, G:E.124, H2O.1, H2O.1, H2O.1 MG.20: 4 residues within 4Å: Chain H: G.157, C.160, V.161, T.163 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:G.157, H:C.160, H:T.163 MG.21: 5 residues within 4Å: Chain I: G.157, C.160, V.161, F.162, T.163 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:G.157, I:C.160, I:T.163 MG.23: 3 residues within 4Å: Chain J: D.123 Ligands: ADP.22, PO4.24 No protein-ligand interaction detected (PLIP) MG.25: 4 residues within 4Å: Chain J: E.124 Chain P: R.146, E.188 Ligands: PO4.24 5 PLIP interactions: 1 interactions with chain J, 1 interactions with chain P, 3 Ligand-Water interactions Metal complexes: J:E.124, P:E.188, H2O.1, H2O.2, H2O.2 MG.27: 4 residues within 4Å: Chain K: G.157, C.160, V.161, T.163 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:G.157, K:C.160, K:T.163 MG.28: 5 residues within 4Å: Chain L: G.157, C.160, V.161, F.162, 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: 4 residues within 4Å: Chain G: R.146, E.188 Chain M: E.124 Ligands: PO4.31 5 PLIP interactions: 1 interactions with chain M, 1 interactions with chain G, 3 Ligand-Water interactions Metal complexes: M:E.124, G:E.188, H2O.1, H2O.1, H2O.2 MG.34: 4 residues within 4Å: Chain N: G.157, C.160, V.161, T.163 3 PLIP interactions: 3 interactions with chain N Metal complexes: N:G.157, N:C.160, N:T.163 MG.35: 5 residues within 4Å: Chain O: G.157, C.160, V.161, F.162, T.163 3 PLIP interactions: 3 interactions with chain O Metal complexes: O:G.157, O:C.160, O:T.163 MG.37: 3 residues within 4Å: Chain P: D.123 Ligands: ADP.36, PO4.38 No protein-ligand interaction detected (PLIP) MG.39: 4 residues within 4Å: Chain M: R.146, E.188 Chain P: E.124 Ligands: PO4.38 5 PLIP interactions: 1 interactions with chain M, 1 interactions with chain P, 3 Ligand-Water interactions Metal complexes: M:E.188, P:E.124, H2O.2, H2O.2, H2O.2 MG.41: 4 residues within 4Å: Chain Q: G.157, C.160, V.161, T.163 3 PLIP interactions: 3 interactions with chain Q Metal complexes: Q:G.157, Q:C.160, Q:T.163 MG.42: 5 residues within 4Å: Chain R: G.157, C.160, V.161, F.162, 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: G.57, P.58, T.59, K.63, E.124 Chain D: E.188 Ligands: ADP.1, MG.2, MG.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.59 Water bridges: A:K.63, A:S.174 Salt bridges: A:K.63 PO4.10: 9 residues within 4Å: Chain D: G.57, P.58, T.59, K.63, E.124 Chain J: E.188 Ligands: ADP.8, MG.9, MG.11 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.59 Water bridges: D:K.63, D:S.174 Salt bridges: D:K.63 PO4.17: 9 residues within 4Å: Chain A: E.188 Chain G: G.57, P.58, T.59, K.63, E.124 Ligands: ADP.15, MG.16, MG.18 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:T.59 Water bridges: G:K.63, G:S.174 Salt bridges: G:K.63 PO4.24: 9 residues within 4Å: Chain J: G.57, P.58, T.59, K.63, E.124 Chain P: E.188 Ligands: ADP.22, MG.23, MG.25 4 PLIP interactions: 4 interactions with chain J Hydrogen bonds: J:T.59 Water bridges: J:K.63, J:S.174 Salt bridges: J:K.63 PO4.31: 9 residues within 4Å: Chain G: E.188 Chain M: G.57, P.58, T.59, K.63, E.124 Ligands: ADP.29, MG.30, MG.32 4 PLIP interactions: 4 interactions with chain M Hydrogen bonds: M:T.59 Water bridges: M:K.63, M:S.174 Salt bridges: M:K.63 PO4.38: 9 residues within 4Å: Chain M: E.188 Chain P: G.57, P.58, T.59, K.63, E.124 Ligands: ADP.36, MG.37, MG.39 4 PLIP interactions: 4 interactions with chain P Hydrogen bonds: P:T.59 Water bridges: P:K.63, P:S.174 Salt bridges: P:K.63

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

LVS.5: 15 residues within 4Å: Chain B: T.1, Q.19, V.20, S.21, M.27, K.33, F.46, A.47, G.48, T.50, G.124, S.125 Chain H: T.107, I.109, D.111 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain H Hydrophobic interactions: B:T.1, B:V.20, B:F.46, B:T.50, H:T.107 Hydrogen bonds: B:S.21, B:S.21, B:G.48, B:T.50 LVS.12: 15 residues within 4Å: Chain B: T.107, I.109, D.111 Chain E: T.1, Q.19, V.20, S.21, M.27, K.33, F.46, A.47, G.48, T.50, G.124, S.125 9 PLIP interactions: 8 interactions with chain E, 1 interactions with chain B Hydrophobic interactions: E:T.1, E:V.20, E:F.46, E:T.50, B:T.107 Hydrogen bonds: E:S.21, E:S.21, E:G.48, E:T.50 LVS.19: 15 residues within 4Å: Chain H: T.1, Q.19, V.20, S.21, M.27, K.33, F.46, A.47, G.48, T.50, G.124, S.125 Chain N: T.107, I.109, D.111 9 PLIP interactions: 8 interactions with chain H, 1 interactions with chain N Hydrophobic interactions: H:T.1, H:V.20, H:F.46, H:T.50, N:T.107 Hydrogen bonds: H:S.21, H:S.21, H:G.48, H:T.50 LVS.26: 15 residues within 4Å: Chain E: T.107, I.109, D.111 Chain K: T.1, Q.19, V.20, S.21, M.27, K.33, F.46, A.47, G.48, T.50, G.124, S.125 9 PLIP interactions: 8 interactions with chain K, 1 interactions with chain E Hydrophobic interactions: K:T.1, K:V.20, K:F.46, K:T.50, E:T.107 Hydrogen bonds: K:S.21, K:S.21, K:G.48, K:T.50 LVS.33: 15 residues within 4Å: Chain N: T.1, Q.19, V.20, S.21, M.27, K.33, F.46, A.47, G.48, T.50, G.124, S.125 Chain Q: T.107, I.109, D.111 9 PLIP interactions: 1 interactions with chain Q, 8 interactions with chain N Hydrophobic interactions: Q:T.107, N:T.1, N:V.20, N:F.46, N:T.50 Hydrogen bonds: N:S.21, N:S.21, N:G.48, N:T.50 LVS.40: 15 residues within 4Å: Chain K: T.107, I.109, D.111 Chain Q: T.1, Q.19, V.20, S.21, M.27, K.33, F.46, A.47, G.48, T.50, G.124, S.125 9 PLIP interactions: 8 interactions with chain Q, 1 interactions with chain K Hydrophobic interactions: Q:T.1, Q:V.20, Q:F.46, Q:T.50, K:T.107 Hydrogen bonds: Q:S.21, Q:S.21, Q:G.48, Q: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: ADGJMP
ATP-DEPENDENT PROTEASE HSLV: BCEFHIKLNOQR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

G
A

J
A

M
A

P
A

B
G

C
L

E
G

F
L

H
G

I
L

K
G

L
L

N
G

O
L

Q
G

R
L

ATP-DEPENDENT HSL PROTEASE ATP-BINDING SUBUNIT HSLU

ATP-DEPENDENT PROTEASE HSLV

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