SMTL ID : 3t63.1

Axial Ligand Swapping In Double Mutant Maintains Intradiol-cleavage Chemistry in Protocatechuate 3,4-Dioxygenase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.54 Å

Oligo State

hetero-12-12-mer

Ligands

48 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.1: 8 residues within 4Å: Chain A: Y.56, D.57, G.60, R.188, I.189, Q.190, G.191, E.192 Ligand excluded by PLIP BME.8: 6 residues within 4Å: Chain A: Y.16 Chain D: Y.108, R.157, H.160, Y.162 Ligands: FE.15 Ligand excluded by PLIP BME.9: 3 residues within 4Å: Chain D: F.56, C.129, L.130 Ligand excluded by PLIP BME.10: 6 residues within 4Å: Chain D: R.150, P.153 Chain E: S.38, I.39, P.40 Chain J: P.215 Ligand excluded by PLIP BME.13: 5 residues within 4Å: Chain A: P.15, R.133 Chain D: Y.24, T.26, W.149 Ligand excluded by PLIP BME.14: 7 residues within 4Å: Chain A: F.200 Chain D: I.10, I.39, P.40, Q.41 Chain F: P.153 Chain R: P.215 Ligand excluded by PLIP BME.16: 9 residues within 4Å: Chain B: P.15, Y.16 Chain E: Y.108, W.149, R.157, H.160, Y.162 Ligands: BME.18, FE.19 Ligand excluded by PLIP BME.17: 3 residues within 4Å: Chain E: F.56, C.129, L.130 Ligand excluded by PLIP BME.18: 6 residues within 4Å: Chain B: P.15, R.133 Chain E: Y.24, T.26, W.149 Ligands: BME.16 Ligand excluded by PLIP BME.20: 9 residues within 4Å: Chain C: P.15, Y.16 Chain F: Y.108, R.157, H.160, Y.162 Ligands: BME.21, BME.22, FE.23 Ligand excluded by PLIP BME.21: 5 residues within 4Å: Chain C: P.15 Chain F: W.149, R.150 Ligands: BME.20, BME.22 Ligand excluded by PLIP BME.22: 9 residues within 4Å: Chain C: G.14, P.15, R.133 Chain F: Y.24, T.26, W.149, I.191 Ligands: BME.20, BME.21 Ligand excluded by PLIP BME.24: 8 residues within 4Å: Chain G: Y.56, D.57, G.60, R.188, I.189, Q.190, G.191, E.192 Ligand excluded by PLIP BME.31: 6 residues within 4Å: Chain G: Y.16 Chain J: Y.108, R.157, H.160, Y.162 Ligands: FE.38 Ligand excluded by PLIP BME.32: 3 residues within 4Å: Chain J: F.56, C.129, L.130 Ligand excluded by PLIP BME.33: 6 residues within 4Å: Chain D: P.215 Chain J: R.150, P.153 Chain K: S.38, I.39, P.40 Ligand excluded by PLIP BME.36: 5 residues within 4Å: Chain G: P.15, R.133 Chain J: Y.24, T.26, W.149 Ligand excluded by PLIP BME.37: 7 residues within 4Å: Chain G: F.200 Chain J: I.10, I.39, P.40, Q.41 Chain L: P.153 Chain X: P.215 Ligand excluded by PLIP BME.39: 9 residues within 4Å: Chain H: P.15, Y.16 Chain K: Y.108, W.149, R.157, H.160, Y.162 Ligands: BME.41, FE.42 Ligand excluded by PLIP BME.40: 3 residues within 4Å: Chain K: F.56, C.129, L.130 Ligand excluded by PLIP BME.41: 6 residues within 4Å: Chain H: P.15, R.133 Chain K: Y.24, T.26, W.149 Ligands: BME.39 Ligand excluded by PLIP BME.43: 9 residues within 4Å: Chain I: P.15, Y.16 Chain L: Y.108, R.157, H.160, Y.162 Ligands: BME.44, BME.45, FE.46 Ligand excluded by PLIP BME.44: 5 residues within 4Å: Chain I: P.15 Chain L: W.149, R.150 Ligands: BME.43, BME.45 Ligand excluded by PLIP BME.45: 9 residues within 4Å: Chain I: G.14, P.15, R.133 Chain L: Y.24, T.26, W.149, I.191 Ligands: BME.43, BME.44 Ligand excluded by PLIP BME.47: 8 residues within 4Å: Chain M: Y.56, D.57, G.60, R.188, I.189, Q.190, G.191, E.192 Ligand excluded by PLIP BME.54: 6 residues within 4Å: Chain M: Y.16 Chain P: Y.108, R.157, H.160, Y.162 Ligands: FE.61 Ligand excluded by PLIP BME.55: 3 residues within 4Å: Chain P: F.56, C.129, L.130 Ligand excluded by PLIP BME.56: 6 residues within 4Å: Chain P: R.150, P.153 Chain Q: S.38, I.39, P.40 Chain V: P.215 Ligand excluded by PLIP BME.59: 5 residues within 4Å: Chain M: P.15, R.133 Chain P: Y.24, T.26, W.149 Ligand excluded by PLIP BME.60: 7 residues within 4Å: Chain F: P.215 Chain M: F.200 Chain P: I.10, I.39, P.40, Q.41 Chain R: P.153 Ligand excluded by PLIP BME.62: 9 residues within 4Å: Chain N: P.15, Y.16 Chain Q: Y.108, W.149, R.157, H.160, Y.162 Ligands: BME.64, FE.65 Ligand excluded by PLIP BME.63: 3 residues within 4Å: Chain Q: F.56, C.129, L.130 Ligand excluded by PLIP BME.64: 6 residues within 4Å: Chain N: P.15, R.133 Chain Q: Y.24, T.26, W.149 Ligands: BME.62 Ligand excluded by PLIP BME.66: 9 residues within 4Å: Chain O: P.15, Y.16 Chain R: Y.108, R.157, H.160, Y.162 Ligands: BME.67, BME.68, FE.69 Ligand excluded by PLIP BME.67: 5 residues within 4Å: Chain O: P.15 Chain R: W.149, R.150 Ligands: BME.66, BME.68 Ligand excluded by PLIP BME.68: 9 residues within 4Å: Chain O: G.14, P.15, R.133 Chain R: Y.24, T.26, W.149, I.191 Ligands: BME.66, BME.67 Ligand excluded by PLIP BME.70: 8 residues within 4Å: Chain S: Y.56, D.57, G.60, R.188, I.189, Q.190, G.191, E.192 Ligand excluded by PLIP BME.77: 6 residues within 4Å: Chain S: Y.16 Chain V: Y.108, R.157, H.160, Y.162 Ligands: FE.84 Ligand excluded by PLIP BME.78: 3 residues within 4Å: Chain V: F.56, C.129, L.130 Ligand excluded by PLIP BME.79: 6 residues within 4Å: Chain P: P.215 Chain V: R.150, P.153 Chain W: S.38, I.39, P.40 Ligand excluded by PLIP BME.82: 5 residues within 4Å: Chain S: P.15, R.133 Chain V: Y.24, T.26, W.149 Ligand excluded by PLIP BME.83: 7 residues within 4Å: Chain L: P.215 Chain S: F.200 Chain V: I.10, I.39, P.40, Q.41 Chain X: P.153 Ligand excluded by PLIP BME.85: 9 residues within 4Å: Chain T: P.15, Y.16 Chain W: Y.108, W.149, R.157, H.160, Y.162 Ligands: BME.87, FE.88 Ligand excluded by PLIP BME.86: 3 residues within 4Å: Chain W: F.56, C.129, L.130 Ligand excluded by PLIP BME.87: 6 residues within 4Å: Chain T: P.15, R.133 Chain W: Y.24, T.26, W.149 Ligands: BME.85 Ligand excluded by PLIP BME.89: 9 residues within 4Å: Chain U: P.15, Y.16 Chain X: Y.108, R.157, H.160, Y.162 Ligands: BME.90, BME.91, FE.92 Ligand excluded by PLIP BME.90: 5 residues within 4Å: Chain U: P.15 Chain X: W.149, R.150 Ligands: BME.89, BME.91 Ligand excluded by PLIP BME.91: 9 residues within 4Å: Chain U: G.14, P.15, R.133 Chain X: Y.24, T.26, W.149, I.191 Ligands: BME.89, BME.90 Ligand excluded by PLIP

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: E.168, T.169, L.170, I.171, A.172, R.184, F.185, D.186, R.188 Ligand excluded by PLIP GOL.4: 7 residues within 4Å: Chain B: E.168, T.169, I.171, R.184, F.185, D.186, R.188 Ligand excluded by PLIP GOL.6: 6 residues within 4Å: Chain C: T.169, I.171, R.184, F.185, D.186, R.188 Ligand excluded by PLIP GOL.11: 6 residues within 4Å: Chain D: Q.203, I.205, K.207, R.222, F.223, D.224 Ligand excluded by PLIP GOL.25: 9 residues within 4Å: Chain G: E.168, T.169, L.170, I.171, A.172, R.184, F.185, D.186, R.188 Ligand excluded by PLIP GOL.27: 7 residues within 4Å: Chain H: E.168, T.169, I.171, R.184, F.185, D.186, R.188 Ligand excluded by PLIP GOL.29: 6 residues within 4Å: Chain I: T.169, I.171, R.184, F.185, D.186, R.188 Ligand excluded by PLIP GOL.34: 6 residues within 4Å: Chain J: Q.203, I.205, K.207, R.222, F.223, D.224 Ligand excluded by PLIP GOL.48: 9 residues within 4Å: Chain M: E.168, T.169, L.170, I.171, A.172, R.184, F.185, D.186, R.188 Ligand excluded by PLIP GOL.50: 7 residues within 4Å: Chain N: E.168, T.169, I.171, R.184, F.185, D.186, R.188 Ligand excluded by PLIP GOL.52: 6 residues within 4Å: Chain O: T.169, I.171, R.184, F.185, D.186, R.188 Ligand excluded by PLIP GOL.57: 6 residues within 4Å: Chain P: Q.203, I.205, K.207, R.222, F.223, D.224 Ligand excluded by PLIP GOL.71: 9 residues within 4Å: Chain S: E.168, T.169, L.170, I.171, A.172, R.184, F.185, D.186, R.188 Ligand excluded by PLIP GOL.73: 7 residues within 4Å: Chain T: E.168, T.169, I.171, R.184, F.185, D.186, R.188 Ligand excluded by PLIP GOL.75: 6 residues within 4Å: Chain U: T.169, I.171, R.184, F.185, D.186, R.188 Ligand excluded by PLIP GOL.80: 6 residues within 4Å: Chain V: Q.203, I.205, K.207, R.222, F.223, D.224 Ligand excluded by PLIP

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

SO4.3: 3 residues within 4Å: Chain A: N.37, T.105, H.107 Ligand excluded by PLIP SO4.5: 4 residues within 4Å: Chain B: N.37, R.38, T.105, H.107 Ligand excluded by PLIP SO4.7: 3 residues within 4Å: Chain C: N.37, T.105, H.107 Ligand excluded by PLIP SO4.12: 1 residues within 4Å: Chain D: R.83 Ligand excluded by PLIP SO4.26: 3 residues within 4Å: Chain G: N.37, T.105, H.107 Ligand excluded by PLIP SO4.28: 4 residues within 4Å: Chain H: N.37, R.38, T.105, H.107 Ligand excluded by PLIP SO4.30: 3 residues within 4Å: Chain I: N.37, T.105, H.107 Ligand excluded by PLIP SO4.35: 1 residues within 4Å: Chain J: R.83 Ligand excluded by PLIP SO4.49: 3 residues within 4Å: Chain M: N.37, T.105, H.107 Ligand excluded by PLIP SO4.51: 4 residues within 4Å: Chain N: N.37, R.38, T.105, H.107 Ligand excluded by PLIP SO4.53: 3 residues within 4Å: Chain O: N.37, T.105, H.107 Ligand excluded by PLIP SO4.58: 1 residues within 4Å: Chain P: R.83 Ligand excluded by PLIP SO4.72: 3 residues within 4Å: Chain S: N.37, T.105, H.107 Ligand excluded by PLIP SO4.74: 4 residues within 4Å: Chain T: N.37, R.38, T.105, H.107 Ligand excluded by PLIP SO4.76: 3 residues within 4Å: Chain U: N.37, T.105, H.107 Ligand excluded by PLIP SO4.81: 1 residues within 4Å: Chain V: R.83 Ligand excluded by PLIP

12 x FE: FE (III) ION(Non-covalent)

FE.15: 5 residues within 4Å: Chain D: Y.108, R.157, H.160, Y.162 Ligands: BME.8 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:Y.108, D:H.160, D:Y.162, H2O.37 FE.19: 5 residues within 4Å: Chain E: Y.108, R.157, H.160, Y.162 Ligands: BME.16 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:Y.108, E:H.160, E:Y.162, H2O.48 FE.23: 5 residues within 4Å: Chain F: Y.108, R.157, H.160, Y.162 Ligands: BME.20 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:Y.108, F:H.160, F:Y.162, H2O.59 FE.38: 5 residues within 4Å: Chain J: Y.108, R.157, H.160, Y.162 Ligands: BME.31 4 PLIP interactions: 3 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:Y.108, J:H.160, J:Y.162, H2O.95 FE.42: 5 residues within 4Å: Chain K: Y.108, R.157, H.160, Y.162 Ligands: BME.39 4 PLIP interactions: 3 interactions with chain K, 1 Ligand-Water interactions Metal complexes: K:Y.108, K:H.160, K:Y.162, H2O.106 FE.46: 5 residues within 4Å: Chain L: Y.108, R.157, H.160, Y.162 Ligands: BME.43 4 PLIP interactions: 3 interactions with chain L, 1 Ligand-Water interactions Metal complexes: L:Y.108, L:H.160, L:Y.162, H2O.117 FE.61: 5 residues within 4Å: Chain P: Y.108, R.157, H.160, Y.162 Ligands: BME.54 4 PLIP interactions: 3 interactions with chain P, 1 Ligand-Water interactions Metal complexes: P:Y.108, P:H.160, P:Y.162, H2O.153 FE.65: 5 residues within 4Å: Chain Q: Y.108, R.157, H.160, Y.162 Ligands: BME.62 4 PLIP interactions: 3 interactions with chain Q, 1 Ligand-Water interactions Metal complexes: Q:Y.108, Q:H.160, Q:Y.162, H2O.164 FE.69: 5 residues within 4Å: Chain R: Y.108, R.157, H.160, Y.162 Ligands: BME.66 4 PLIP interactions: 3 interactions with chain R, 1 Ligand-Water interactions Metal complexes: R:Y.108, R:H.160, R:Y.162, H2O.175 FE.84: 5 residues within 4Å: Chain V: Y.108, R.157, H.160, Y.162 Ligands: BME.77 4 PLIP interactions: 3 interactions with chain V, 1 Ligand-Water interactions Metal complexes: V:Y.108, V:H.160, V:Y.162, H2O.211 FE.88: 5 residues within 4Å: Chain W: Y.108, R.157, H.160, Y.162 Ligands: BME.85 4 PLIP interactions: 3 interactions with chain W, 1 Ligand-Water interactions Metal complexes: W:Y.108, W:H.160, W:Y.162, H2O.223 FE.92: 5 residues within 4Å: Chain X: Y.108, R.157, H.160, Y.162 Ligands: BME.89 4 PLIP interactions: 3 interactions with chain X, 1 Ligand-Water interactions Metal complexes: X:Y.108, X:H.160, X:Y.162, H2O.233

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Purpero, V.M. et al., Axial Ligand Swapping In Double Mutant Maintains Intradiol-cleavage Chemistry in Protocatechuate 3,4-Dioxygenase. To be Published

Release Date

2012-08-01

Peptides

Protocatechuate 3,4-dioxygenase alpha chain: ABCGHIMNOSTU
Protocatechuate 3,4-dioxygenase beta chain: DEFJKLPQRVWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

G
A

H
B

I
C

M
A

N
B

O
C

S
A

T
B

U
C

D
M

E
N

F
O

J
M

K
N

L
O

P
M

Q
N

R
O

V
M

W
N

X
O

Protocatechuate 3,4-dioxygenase alpha chain

Protocatechuate 3,4-dioxygenase beta chain

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