SMTL ID : 3p2l.1

Crystal Structure of ATP-dependent Clp protease subunit P from Francisella tularensis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-14-mer

Ligands

14 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: M.84, Q.85, I.87, P.89 Ligands: PO4.11 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:M.84, A:I.87, A:P.89, H2O.47 MG.12: 5 residues within 4Å: Chain B: M.84, Q.85, I.87, P.89 Ligands: PO4.14 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:M.84, B:I.87, B:P.89, H2O.74 MG.22: 6 residues within 4Å: Chain C: M.84, Q.85, I.87, K.88, P.89 Ligands: PO4.29 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:M.84, C:I.87, C:P.89, H2O.151 MG.30: 5 residues within 4Å: Chain D: M.84, Q.85, I.87, P.89 Ligands: PO4.37 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:M.84, D:I.87, D:P.89, H2O.172 MG.38: 4 residues within 4Å: Chain E: M.84, I.87, P.89 Ligands: PO4.46 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:M.84, E:I.87, E:P.89, H2O.216 MG.47: 5 residues within 4Å: Chain F: M.84, I.87, K.88, P.89 Ligands: PO4.53 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:M.84, F:I.87, F:P.89 MG.54: 5 residues within 4Å: Chain G: M.84, Q.85, I.87, P.89 Ligands: PO4.63 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:M.84, G:I.87, G:P.89, H2O.305 MG.64: 5 residues within 4Å: Chain H: M.84, Q.85, I.87, P.89 Ligands: PO4.74 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:M.84, H:I.87, H:P.89, H2O.396 MG.75: 5 residues within 4Å: Chain I: M.84, Q.85, I.87, P.89 Ligands: PO4.77 4 PLIP interactions: 3 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:M.84, I:I.87, I:P.89, H2O.423 MG.85: 6 residues within 4Å: Chain J: M.84, Q.85, I.87, K.88, P.89 Ligands: PO4.92 4 PLIP interactions: 3 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:M.84, J:I.87, J:P.89, H2O.500 MG.93: 5 residues within 4Å: Chain K: M.84, Q.85, I.87, P.89 Ligands: PO4.100 4 PLIP interactions: 3 interactions with chain K, 1 Ligand-Water interactions Metal complexes: K:M.84, K:I.87, K:P.89, H2O.521 MG.101: 4 residues within 4Å: Chain L: M.84, I.87, P.89 Ligands: PO4.109 4 PLIP interactions: 3 interactions with chain L, 1 Ligand-Water interactions Metal complexes: L:M.84, L:I.87, L:P.89, H2O.565 MG.110: 5 residues within 4Å: Chain M: M.84, I.87, K.88, P.89 Ligands: PO4.116 3 PLIP interactions: 3 interactions with chain M Metal complexes: M:M.84, M:I.87, M:P.89 MG.117: 5 residues within 4Å: Chain N: M.84, Q.85, I.87, P.89 Ligands: PO4.126 4 PLIP interactions: 3 interactions with chain N, 1 Ligand-Water interactions Metal complexes: N:M.84, N:I.87, N:P.89, H2O.654

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

PEG.2: 4 residues within 4Å: Chain A: I.32, Y.66, I.193, R.196 Ligand excluded by PLIP PEG.4: 4 residues within 4Å: Chain A: P.70, G.71, G.72, S.101 Ligand excluded by PLIP PEG.6: 3 residues within 4Å: Chain A: Y.81 Chain D: P.119, S.120 Ligand excluded by PLIP PEG.15: 5 residues within 4Å: Chain B: Y.64, Y.66, Y.116, I.193, R.196 Ligand excluded by PLIP PEG.16: 9 residues within 4Å: Chain B: V.74, S.101, S.104, H.126, Q.127, P.128, L.129, L.153 Ligands: PEG.17 Ligand excluded by PLIP PEG.17: 6 residues within 4Å: Chain B: P.70, G.71, G.72, S.101, L.129 Ligands: PEG.16 Ligand excluded by PLIP PEG.21: 5 residues within 4Å: Chain B: T.161, G.162, K.184, A.185, G.187 Ligand excluded by PLIP PEG.23: 4 residues within 4Å: Chain C: Y.64, Y.66, I.94, R.196 Ligand excluded by PLIP PEG.24: 9 residues within 4Å: Chain C: S.101, M.102, S.104, I.125, H.126, Q.127, P.128, L.153, L.157 Ligand excluded by PLIP PEG.26: 3 residues within 4Å: Chain C: K.184, H.191, V.192 Ligand excluded by PLIP PEG.31: 3 residues within 4Å: Chain D: Y.64, Y.66, R.196 Ligand excluded by PLIP PEG.32: 6 residues within 4Å: Chain D: E.38, P.70, G.71, G.72, S.101, L.129 Ligand excluded by PLIP PEG.34: 6 residues within 4Å: Chain A: R.148 Chain D: D.171, N.176, F.177, M.178, Y.186 Ligand excluded by PLIP PEG.36: 4 residues within 4Å: Chain D: T.161, Q.163, A.185, G.187 Ligand excluded by PLIP PEG.39: 3 residues within 4Å: Chain E: Y.64, Y.66, R.196 Ligand excluded by PLIP PEG.40: 10 residues within 4Å: Chain E: V.74, S.101, M.102, S.104, I.125, H.126, Q.127, P.128, L.153, L.157 Ligand excluded by PLIP PEG.41: 6 residues within 4Å: Chain E: E.38, P.70, G.71, G.72, S.101, L.129 Ligand excluded by PLIP PEG.42: 3 residues within 4Å: Chain E: N.176, F.177, E.182 Ligand excluded by PLIP PEG.48: 4 residues within 4Å: Chain F: P.70, G.71, G.72, S.101 Ligand excluded by PLIP PEG.49: 9 residues within 4Å: Chain F: S.101, M.102, S.104, I.125, H.126, Q.127, P.128, L.153, L.157 Ligand excluded by PLIP PEG.52: 3 residues within 4Å: Chain F: Y.64, Y.66, R.196 Ligand excluded by PLIP PEG.55: 6 residues within 4Å: Chain G: I.32, Y.64, Y.66, I.94, Y.116, R.196 Ligand excluded by PLIP PEG.56: 8 residues within 4Å: Chain G: S.101, M.102, S.104, I.125, H.126, Q.127, P.128, L.157 Ligand excluded by PLIP PEG.57: 6 residues within 4Å: Chain G: E.38, P.70, G.71, G.72, S.101, L.129 Ligand excluded by PLIP PEG.58: 5 residues within 4Å: Chain G: D.171, N.176, F.177, M.178, E.182 Ligand excluded by PLIP PEG.61: 6 residues within 4Å: Chain G: T.161, Q.163, K.184, A.185, Y.186, G.187 Ligand excluded by PLIP PEG.65: 4 residues within 4Å: Chain H: I.32, Y.66, I.193, R.196 Ligand excluded by PLIP PEG.67: 4 residues within 4Å: Chain H: P.70, G.71, G.72, S.101 Ligand excluded by PLIP PEG.69: 3 residues within 4Å: Chain H: Y.81 Chain K: P.119, S.120 Ligand excluded by PLIP PEG.78: 5 residues within 4Å: Chain I: Y.64, Y.66, Y.116, I.193, R.196 Ligand excluded by PLIP PEG.79: 9 residues within 4Å: Chain I: V.74, S.101, S.104, H.126, Q.127, P.128, L.129, L.153 Ligands: PEG.80 Ligand excluded by PLIP PEG.80: 6 residues within 4Å: Chain I: P.70, G.71, G.72, S.101, L.129 Ligands: PEG.79 Ligand excluded by PLIP PEG.84: 5 residues within 4Å: Chain I: T.161, G.162, K.184, A.185, G.187 Ligand excluded by PLIP PEG.86: 4 residues within 4Å: Chain J: Y.64, Y.66, I.94, R.196 Ligand excluded by PLIP PEG.87: 9 residues within 4Å: Chain J: S.101, M.102, S.104, I.125, H.126, Q.127, P.128, L.153, L.157 Ligand excluded by PLIP PEG.89: 3 residues within 4Å: Chain J: K.184, H.191, V.192 Ligand excluded by PLIP PEG.94: 3 residues within 4Å: Chain K: Y.64, Y.66, R.196 Ligand excluded by PLIP PEG.95: 6 residues within 4Å: Chain K: E.38, P.70, G.71, G.72, S.101, L.129 Ligand excluded by PLIP PEG.97: 6 residues within 4Å: Chain H: R.148 Chain K: D.171, N.176, F.177, M.178, Y.186 Ligand excluded by PLIP PEG.99: 4 residues within 4Å: Chain K: T.161, Q.163, A.185, G.187 Ligand excluded by PLIP PEG.102: 3 residues within 4Å: Chain L: Y.64, Y.66, R.196 Ligand excluded by PLIP PEG.103: 10 residues within 4Å: Chain L: V.74, S.101, M.102, S.104, I.125, H.126, Q.127, P.128, L.153, L.157 Ligand excluded by PLIP PEG.104: 6 residues within 4Å: Chain L: E.38, P.70, G.71, G.72, S.101, L.129 Ligand excluded by PLIP PEG.105: 3 residues within 4Å: Chain L: N.176, F.177, E.182 Ligand excluded by PLIP PEG.111: 4 residues within 4Å: Chain M: P.70, G.71, G.72, S.101 Ligand excluded by PLIP PEG.112: 9 residues within 4Å: Chain M: S.101, M.102, S.104, I.125, H.126, Q.127, P.128, L.153, L.157 Ligand excluded by PLIP PEG.115: 3 residues within 4Å: Chain M: Y.64, Y.66, R.196 Ligand excluded by PLIP PEG.118: 6 residues within 4Å: Chain N: I.32, Y.64, Y.66, I.94, Y.116, R.196 Ligand excluded by PLIP PEG.119: 8 residues within 4Å: Chain N: S.101, M.102, S.104, I.125, H.126, Q.127, P.128, L.157 Ligand excluded by PLIP PEG.120: 6 residues within 4Å: Chain N: E.38, P.70, G.71, G.72, S.101, L.129 Ligand excluded by PLIP PEG.121: 5 residues within 4Å: Chain N: D.171, N.176, F.177, M.178, E.182 Ligand excluded by PLIP PEG.124: 6 residues within 4Å: Chain N: T.161, Q.163, K.184, A.185, Y.186, G.187 Ligand excluded by PLIP

30 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: S.101, M.102, S.104, I.125, H.126, L.157 Ligand excluded by PLIP GOL.5: 5 residues within 4Å: Chain A: D.171, N.176, F.177, M.178, E.182 Ligand excluded by PLIP GOL.8: 7 residues within 4Å: Chain A: T.161, G.162, Q.163, A.185, Y.186, G.187 Ligands: GOL.10 Ligand excluded by PLIP GOL.10: 5 residues within 4Å: Chain A: K.112, R.115, H.160, T.161 Ligands: GOL.8 Ligand excluded by PLIP GOL.18: 5 residues within 4Å: Chain B: N.176, F.177, M.178, E.182 Chain C: R.148 Ligand excluded by PLIP GOL.19: 5 residues within 4Å: Chain B: Y.24, F.34, N.36 Chain C: N.45 Chain N: L.6 Ligand excluded by PLIP GOL.25: 5 residues within 4Å: Chain C: E.38, P.70, G.71, G.72, S.101 Ligand excluded by PLIP GOL.28: 4 residues within 4Å: Chain C: Y.24, F.34, L.35, N.36 Ligand excluded by PLIP GOL.33: 8 residues within 4Å: Chain D: S.101, M.102, S.104, I.125, H.126, Q.127, P.128, L.153 Ligand excluded by PLIP GOL.35: 3 residues within 4Å: Chain D: K.184, H.191, V.192 Ligand excluded by PLIP GOL.43: 5 residues within 4Å: Chain E: T.161, G.162, Q.163, A.185, G.187 Ligand excluded by PLIP GOL.44: 4 residues within 4Å: Chain E: Y.24, F.34, N.36 Chain M: N.45 Ligand excluded by PLIP GOL.45: 4 residues within 4Å: Chain E: K.112, R.115, H.160, T.161 Ligand excluded by PLIP GOL.50: 4 residues within 4Å: Chain F: N.176, F.177, M.178, E.182 Ligand excluded by PLIP GOL.62: 3 residues within 4Å: Chain G: F.34, N.36 Chain I: N.45 Ligand excluded by PLIP GOL.66: 6 residues within 4Å: Chain H: S.101, M.102, S.104, I.125, H.126, L.157 Ligand excluded by PLIP GOL.68: 5 residues within 4Å: Chain H: D.171, N.176, F.177, M.178, E.182 Ligand excluded by PLIP GOL.71: 7 residues within 4Å: Chain H: T.161, G.162, Q.163, A.185, Y.186, G.187 Ligands: GOL.73 Ligand excluded by PLIP GOL.73: 5 residues within 4Å: Chain H: K.112, R.115, H.160, T.161 Ligands: GOL.71 Ligand excluded by PLIP GOL.81: 5 residues within 4Å: Chain I: N.176, F.177, M.178, E.182 Chain J: R.148 Ligand excluded by PLIP GOL.82: 5 residues within 4Å: Chain G: L.6 Chain I: Y.24, F.34, N.36 Chain J: N.45 Ligand excluded by PLIP GOL.88: 5 residues within 4Å: Chain J: E.38, P.70, G.71, G.72, S.101 Ligand excluded by PLIP GOL.91: 4 residues within 4Å: Chain J: Y.24, F.34, L.35, N.36 Ligand excluded by PLIP GOL.96: 8 residues within 4Å: Chain K: S.101, M.102, S.104, I.125, H.126, Q.127, P.128, L.153 Ligand excluded by PLIP GOL.98: 3 residues within 4Å: Chain K: K.184, H.191, V.192 Ligand excluded by PLIP GOL.106: 5 residues within 4Å: Chain L: T.161, G.162, Q.163, A.185, G.187 Ligand excluded by PLIP GOL.107: 4 residues within 4Å: Chain F: N.45 Chain L: Y.24, F.34, N.36 Ligand excluded by PLIP GOL.108: 4 residues within 4Å: Chain L: K.112, R.115, H.160, T.161 Ligand excluded by PLIP GOL.113: 4 residues within 4Å: Chain M: N.176, F.177, M.178, E.182 Ligand excluded by PLIP GOL.125: 3 residues within 4Å: Chain B: N.45 Chain N: F.34, N.36 Ligand excluded by PLIP

10 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 3 residues within 4Å: Chain A: K.184, H.191, V.192 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.184, A:H.191, A:V.192, A:V.192 EDO.9: 1 residues within 4Å: Chain A: F.34 4 PLIP interactions: 4 interactions with chain A Water bridges: A:F.34, A:N.36, A:N.36, A:Q.50 EDO.27: 4 residues within 4Å: Chain C: K.112, H.160, T.161, G.162 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.112, C:R.115 EDO.51: 5 residues within 4Å: Chain F: T.161, Q.163, A.185, Y.186, G.187 1 PLIP interactions: 1 interactions with chain F Water bridges: F:G.187 EDO.60: 4 residues within 4Å: Chain G: K.112, H.160, T.161, G.162 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:K.112 EDO.70: 3 residues within 4Å: Chain H: K.184, H.191, V.192 4 PLIP interactions: 4 interactions with chain H Hydrogen bonds: H:K.184, H:H.191, H:V.192, H:V.192 EDO.72: 1 residues within 4Å: Chain H: F.34 4 PLIP interactions: 4 interactions with chain H Water bridges: H:F.34, H:N.36, H:N.36, H:Q.50 EDO.90: 4 residues within 4Å: Chain J: K.112, H.160, T.161, G.162 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:K.112, J:R.115 EDO.114: 5 residues within 4Å: Chain M: T.161, Q.163, A.185, Y.186, G.187 1 PLIP interactions: 1 interactions with chain M Water bridges: M:G.187 EDO.123: 4 residues within 4Å: Chain N: K.112, H.160, T.161, G.162 1 PLIP interactions: 1 interactions with chain N Hydrogen bonds: N:K.112

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

PO4.11: 6 residues within 4Å: Chain A: Q.85, I.87, K.88, P.89, D.90 Ligands: MG.1 Ligand excluded by PLIP PO4.13: 3 residues within 4Å: Chain B: K.184, D.190, H.191 Ligand excluded by PLIP PO4.14: 7 residues within 4Å: Chain B: Q.85, I.87, K.88, P.89, D.90 Chain N: S.195 Ligands: MG.12 Ligand excluded by PLIP PO4.20: 2 residues within 4Å: Chain B: K.155, V.156 Ligand excluded by PLIP PO4.29: 6 residues within 4Å: Chain B: S.195 Chain C: Q.85, I.87, K.88, D.90 Ligands: MG.22 Ligand excluded by PLIP PO4.37: 6 residues within 4Å: Chain D: Q.85, I.87, K.88, P.89, D.90 Ligands: MG.30 Ligand excluded by PLIP PO4.46: 7 residues within 4Å: Chain C: S.195, E.197 Chain E: Q.85, I.87, K.88, D.90 Ligands: MG.38 Ligand excluded by PLIP PO4.53: 6 residues within 4Å: Chain F: Q.85, I.87, K.88, D.90 Chain L: E.197 Ligands: MG.47 Ligand excluded by PLIP PO4.59: 3 residues within 4Å: Chain G: K.184, H.191, V.192 Ligand excluded by PLIP PO4.63: 6 residues within 4Å: Chain G: Q.85, I.87, K.88, P.89, D.90 Ligands: MG.54 Ligand excluded by PLIP PO4.74: 6 residues within 4Å: Chain H: Q.85, I.87, K.88, P.89, D.90 Ligands: MG.64 Ligand excluded by PLIP PO4.76: 3 residues within 4Å: Chain I: K.184, D.190, H.191 Ligand excluded by PLIP PO4.77: 7 residues within 4Å: Chain G: S.195 Chain I: Q.85, I.87, K.88, P.89, D.90 Ligands: MG.75 Ligand excluded by PLIP PO4.83: 2 residues within 4Å: Chain I: K.155, V.156 Ligand excluded by PLIP PO4.92: 6 residues within 4Å: Chain I: S.195 Chain J: Q.85, I.87, K.88, D.90 Ligands: MG.85 Ligand excluded by PLIP PO4.100: 6 residues within 4Å: Chain K: Q.85, I.87, K.88, P.89, D.90 Ligands: MG.93 Ligand excluded by PLIP PO4.109: 7 residues within 4Å: Chain J: S.195, E.197 Chain L: Q.85, I.87, K.88, D.90 Ligands: MG.101 Ligand excluded by PLIP PO4.116: 6 residues within 4Å: Chain E: E.197 Chain M: Q.85, I.87, K.88, D.90 Ligands: MG.110 Ligand excluded by PLIP PO4.122: 3 residues within 4Å: Chain N: K.184, H.191, V.192 Ligand excluded by PLIP PO4.126: 6 residues within 4Å: Chain N: Q.85, I.87, K.88, P.89, D.90 Ligands: MG.117 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y. et al., Crystal Structure of ATP-dependent Clp protease subunit P from Francisella tularensis. To be Published

Release Date

2010-10-20

Peptides

ATP-dependent Clp protease proteolytic subunit: ABCDEFGHIJKLMN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
A

I
B

J
C

K
D

L
E

M
F

N
G

ATP-dependent Clp protease proteolytic subunit