SMTL ID : 3ij3.3 (2 other biounits)

1.8 Angstrom Resolution Crystal Structure of Cytosol Aminopeptidase from Coxiella burnetii

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

CL.1: 5 residues within 4Å: Chain A: L.176, I.177, T.179, K.271, M.274 Ligand excluded by PLIP CL.17: 5 residues within 4Å: Chain B: L.176, I.177, T.179, K.271, M.274 Ligand excluded by PLIP

2 x LI: LITHIUM ION(Non-covalent)

LI.2: 6 residues within 4Å: Chain A: K.250, D.255, D.273, E.334, T.361 Ligands: SO4.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.255, A:D.273, A:E.334, H2O.1 LI.18: 6 residues within 4Å: Chain B: K.250, D.255, D.273, E.334, T.361 Ligands: SO4.19 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.255, B:D.273, B:E.334, H2O.17

10 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 10 residues within 4Å: Chain A: K.250, D.332, A.333, E.334, G.335, R.336, S.358, T.359, R.365 Ligands: LI.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:E.334, A:G.335, A:R.336, A:S.358 Water bridges: A:K.250, A:K.250, A:R.336, A:T.361 Salt bridges: A:K.250, A:R.336, A:R.365 SO4.4: 3 residues within 4Å: Chain A: G.308, S.309, R.310 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.309 Water bridges: A:R.310, A:R.310 SO4.5: 6 residues within 4Å: Chain A: R.336, R.365, S.420, S.421, G.427, T.430 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.421, A:S.421, A:T.430 Water bridges: A:N.330 Salt bridges: A:R.336 SO4.6: 5 residues within 4Å: Chain A: K.203, K.236, I.240, R.295, E.349 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.236 Salt bridges: A:K.203, A:K.236, A:R.295 SO4.7: 3 residues within 4Å: Chain A: K.161, R.162, Q.290 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Q.290 Water bridges: A:K.161, A:K.161, A:K.161, A:R.162, A:R.162 Salt bridges: A:K.161, A:R.162 SO4.19: 10 residues within 4Å: Chain B: K.250, D.332, A.333, E.334, G.335, R.336, S.358, T.359, R.365 Ligands: LI.18 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:E.334, B:G.335, B:R.336, B:S.358 Water bridges: B:K.250, B:K.250, B:T.361, B:T.361 Salt bridges: B:K.250, B:R.336, B:R.365 SO4.20: 3 residues within 4Å: Chain B: G.308, S.309, R.310 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.309 Water bridges: B:R.310, B:R.310 SO4.21: 6 residues within 4Å: Chain B: R.336, R.365, S.420, S.421, G.427, T.430 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.421, B:S.421 Water bridges: B:N.330 Salt bridges: B:R.336 SO4.22: 5 residues within 4Å: Chain B: K.203, K.236, I.240, R.295, E.349 4 PLIP interactions: 4 interactions with chain B Water bridges: B:K.236 Salt bridges: B:K.203, B:K.236, B:R.295 SO4.23: 3 residues within 4Å: Chain B: K.161, R.162, Q.290 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.290 Water bridges: B:K.161, B:K.161, B:K.161, B:R.162 Salt bridges: B:K.161, B:R.162

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

EDO.8: 4 residues within 4Å: Chain A: R.407, L.410, K.411, H.437 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.407, A:H.437 EDO.9: 3 residues within 4Å: Chain A: S.147, P.148, Y.149 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.148 Water bridges: A:L.150 EDO.10: 3 residues within 4Å: Chain A: T.214, E.215, T.320 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.320 Water bridges: A:T.320 EDO.24: 4 residues within 4Å: Chain B: R.407, L.410, K.411, H.437 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.407, B:H.437 EDO.25: 3 residues within 4Å: Chain B: S.147, P.148, Y.149 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.148 Water bridges: B:L.150 EDO.26: 3 residues within 4Å: Chain B: T.214, E.215, T.320 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.320 Water bridges: B:T.320

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

PEG.11: 4 residues within 4Å: Chain A: L.172, L.176, T.179, M.184 No protein-ligand interaction detected (PLIP) PEG.27: 4 residues within 4Å: Chain B: L.172, L.176, T.179, M.184 No protein-ligand interaction detected (PLIP)

4 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.12: 5 residues within 4Å: Chain A: A.322, R.323, K.324, D.416, H.437 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.324 PGE.13: 5 residues within 4Å: Chain A: S.381, L.382, A.385, Y.476, Q.480 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.379 Water bridges: A:S.381 PGE.28: 5 residues within 4Å: Chain B: A.322, R.323, K.324, D.416, H.437 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.324 PGE.29: 5 residues within 4Å: Chain B: S.381, L.382, A.385, Y.476, Q.480 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.379, B:Y.476 Water bridges: B:S.381

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

PG4.14: 7 residues within 4Å: Chain A: E.201, K.203, K.236, W.237, G.238, D.239, R.295 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.203, A:G.238, A:R.295, A:R.295 PG4.15: 12 residues within 4Å: Chain A: A.322, K.324, A.344, V.347, Q.404, R.407, Q.436, H.437, F.438, V.439, S.440, D.441 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.404 Water bridges: A:K.324, A:R.407, A:R.407, A:Q.436, A:D.441, A:D.441 PG4.16: 9 residues within 4Å: Chain A: S.390, L.391, D.394, P.396, L.397, W.398 Chain B: P.401, L.402, F.403 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.394, A:D.394 Water bridges: A:D.394 PG4.30: 7 residues within 4Å: Chain B: E.201, K.203, K.236, W.237, G.238, D.239, R.295 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.203, B:G.238, B:R.295, B:R.295 PG4.31: 12 residues within 4Å: Chain B: A.322, K.324, A.344, V.347, Q.404, R.407, Q.436, H.437, F.438, V.439, S.440, D.441 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.404 Water bridges: B:K.324, B:R.407, B:R.407, B:Q.436, B:D.441, B:D.441 PG4.32: 9 residues within 4Å: Chain A: P.401, L.402, F.403 Chain B: S.390, L.391, D.394, P.396, L.397, W.398 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.394 Water bridges: B:D.394

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Minasov, G. et al., 1.8 Angstrom Resolution Crystal Structure of Cytosol Aminopeptidase from Coxiella burnetii. TO BE PUBLISHED

Release Date

2009-08-11

Peptides

Cytosol aminopeptidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Cytosol aminopeptidase

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