SMTL ID : 3mi1.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

hetero-12-12-mer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: N.37, R.38, T.105, H.107 Ligand excluded by PLIP SO4.3: 5 residues within 4Å: Chain A: P.15, R.133 Chain B: Y.24, T.26, W.149 Ligand excluded by PLIP SO4.10: 4 residues within 4Å: Chain C: N.37, R.38, T.105, H.107 Ligand excluded by PLIP SO4.11: 4 residues within 4Å: Chain C: R.133 Chain D: Y.24, T.26, W.149 Ligand excluded by PLIP SO4.14: 2 residues within 4Å: Chain D: R.114, R.150 Ligand excluded by PLIP SO4.18: 3 residues within 4Å: Chain E: N.37, T.105, H.107 Ligand excluded by PLIP SO4.19: 6 residues within 4Å: Chain E: P.15, R.133, G.134 Chain F: Y.24, T.26, W.149 Ligand excluded by PLIP SO4.27: 3 residues within 4Å: Chain F: N.112, R.114, R.150 Ligand excluded by PLIP SO4.30: 4 residues within 4Å: Chain G: N.37, R.38, T.105, H.107 Ligand excluded by PLIP SO4.32: 5 residues within 4Å: Chain G: P.15, R.133 Chain H: Y.24, T.26, W.149 Ligand excluded by PLIP SO4.39: 4 residues within 4Å: Chain I: N.37, R.38, T.105, H.107 Ligand excluded by PLIP SO4.40: 4 residues within 4Å: Chain I: R.133 Chain J: Y.24, T.26, W.149 Ligand excluded by PLIP SO4.43: 2 residues within 4Å: Chain J: R.114, R.150 Ligand excluded by PLIP SO4.47: 3 residues within 4Å: Chain K: N.37, T.105, H.107 Ligand excluded by PLIP SO4.48: 6 residues within 4Å: Chain K: P.15, R.133, G.134 Chain L: Y.24, T.26, W.149 Ligand excluded by PLIP SO4.56: 3 residues within 4Å: Chain L: N.112, R.114, R.150 Ligand excluded by PLIP SO4.59: 4 residues within 4Å: Chain M: N.37, R.38, T.105, H.107 Ligand excluded by PLIP SO4.61: 5 residues within 4Å: Chain M: P.15, R.133 Chain N: Y.24, T.26, W.149 Ligand excluded by PLIP SO4.68: 4 residues within 4Å: Chain O: N.37, R.38, T.105, H.107 Ligand excluded by PLIP SO4.69: 4 residues within 4Å: Chain O: R.133 Chain P: Y.24, T.26, W.149 Ligand excluded by PLIP SO4.72: 2 residues within 4Å: Chain P: R.114, R.150 Ligand excluded by PLIP SO4.76: 3 residues within 4Å: Chain Q: N.37, T.105, H.107 Ligand excluded by PLIP SO4.77: 6 residues within 4Å: Chain Q: P.15, R.133, G.134 Chain R: Y.24, T.26, W.149 Ligand excluded by PLIP SO4.85: 3 residues within 4Å: Chain R: N.112, R.114, R.150 Ligand excluded by PLIP SO4.88: 4 residues within 4Å: Chain S: N.37, R.38, T.105, H.107 Ligand excluded by PLIP SO4.90: 5 residues within 4Å: Chain S: P.15, R.133 Chain T: Y.24, T.26, W.149 Ligand excluded by PLIP SO4.97: 4 residues within 4Å: Chain U: N.37, R.38, T.105, H.107 Ligand excluded by PLIP SO4.98: 4 residues within 4Å: Chain U: R.133 Chain V: Y.24, T.26, W.149 Ligand excluded by PLIP SO4.101: 2 residues within 4Å: Chain V: R.114, R.150 Ligand excluded by PLIP SO4.105: 3 residues within 4Å: Chain W: N.37, T.105, H.107 Ligand excluded by PLIP SO4.106: 6 residues within 4Å: Chain W: P.15, R.133, G.134 Chain X: Y.24, T.26, W.149 Ligand excluded by PLIP SO4.114: 3 residues within 4Å: Chain X: N.112, R.114, R.150 Ligand excluded by PLIP

24 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: T.169, I.171, R.184, F.185, D.186, R.188 Ligand excluded by PLIP GOL.5: 7 residues within 4Å: Chain B: Q.203, I.205, K.207, R.222, F.223, D.224 Chain I: I.2 Ligand excluded by PLIP GOL.12: 6 residues within 4Å: Chain C: T.169, I.171, R.184, F.185, D.186, R.188 Ligand excluded by PLIP GOL.16: 8 residues within 4Å: Chain D: Q.202, Q.203, I.205, K.207, R.222, F.223, D.224 Chain W: I.2 Ligand excluded by PLIP GOL.20: 6 residues within 4Å: Chain E: T.169, I.171, R.184, F.185, D.186, R.188 Ligand excluded by PLIP GOL.24: 7 residues within 4Å: Chain F: Q.203, I.205, K.207, R.222, F.223, D.224 Chain M: I.2 Ligand excluded by PLIP GOL.31: 6 residues within 4Å: Chain G: T.169, I.171, R.184, F.185, D.186, R.188 Ligand excluded by PLIP GOL.34: 7 residues within 4Å: Chain C: I.2 Chain H: Q.203, I.205, K.207, R.222, F.223, D.224 Ligand excluded by PLIP GOL.41: 6 residues within 4Å: Chain I: T.169, I.171, R.184, F.185, D.186, R.188 Ligand excluded by PLIP GOL.45: 8 residues within 4Å: Chain J: Q.202, Q.203, I.205, K.207, R.222, F.223, D.224 Chain Q: I.2 Ligand excluded by PLIP GOL.49: 6 residues within 4Å: Chain K: T.169, I.171, R.184, F.185, D.186, R.188 Ligand excluded by PLIP GOL.53: 7 residues within 4Å: Chain L: Q.203, I.205, K.207, R.222, F.223, D.224 Chain S: I.2 Ligand excluded by PLIP GOL.60: 6 residues within 4Å: Chain M: T.169, I.171, R.184, F.185, D.186, R.188 Ligand excluded by PLIP GOL.63: 7 residues within 4Å: Chain N: Q.203, I.205, K.207, R.222, F.223, D.224 Chain U: I.2 Ligand excluded by PLIP GOL.70: 6 residues within 4Å: Chain O: T.169, I.171, R.184, F.185, D.186, R.188 Ligand excluded by PLIP GOL.74: 8 residues within 4Å: Chain K: I.2 Chain P: Q.202, Q.203, I.205, K.207, R.222, F.223, D.224 Ligand excluded by PLIP GOL.78: 6 residues within 4Å: Chain Q: T.169, I.171, R.184, F.185, D.186, R.188 Ligand excluded by PLIP GOL.82: 7 residues within 4Å: Chain A: I.2 Chain R: Q.203, I.205, K.207, R.222, F.223, D.224 Ligand excluded by PLIP GOL.89: 6 residues within 4Å: Chain S: T.169, I.171, R.184, F.185, D.186, R.188 Ligand excluded by PLIP GOL.92: 7 residues within 4Å: Chain O: I.2 Chain T: Q.203, I.205, K.207, R.222, F.223, D.224 Ligand excluded by PLIP GOL.99: 6 residues within 4Å: Chain U: T.169, I.171, R.184, F.185, D.186, R.188 Ligand excluded by PLIP GOL.103: 8 residues within 4Å: Chain E: I.2 Chain V: Q.202, Q.203, I.205, K.207, R.222, F.223, D.224 Ligand excluded by PLIP GOL.107: 6 residues within 4Å: Chain W: T.169, I.171, R.184, F.185, D.186, R.188 Ligand excluded by PLIP GOL.111: 7 residues within 4Å: Chain G: I.2 Chain X: Q.203, I.205, K.207, R.222, F.223, D.224 Ligand excluded by PLIP

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

FE.4: 6 residues within 4Å: Chain A: T.12, G.14 Chain B: R.157, Y.162, Q.177, I.191 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:Y.162, H2O.7, H2O.17 FE.13: 6 residues within 4Å: Chain C: T.12, G.14 Chain D: R.157, Y.162, Q.177, I.191 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:Y.162, H2O.25, H2O.34 FE.23: 6 residues within 4Å: Chain E: T.12, G.14 Chain F: R.157, Y.162, Q.177, I.191 3 PLIP interactions: 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:Y.162, H2O.42, H2O.52 FE.33: 6 residues within 4Å: Chain G: T.12, G.14 Chain H: R.157, Y.162, Q.177, I.191 3 PLIP interactions: 1 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:Y.162, H2O.59, H2O.69 FE.42: 6 residues within 4Å: Chain I: T.12, G.14 Chain J: R.157, Y.162, Q.177, I.191 3 PLIP interactions: 1 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:Y.162, H2O.77, H2O.87 FE.52: 6 residues within 4Å: Chain K: T.12, G.14 Chain L: R.157, Y.162, Q.177, I.191 3 PLIP interactions: 1 interactions with chain L, 2 Ligand-Water interactions Metal complexes: L:Y.162, H2O.94, H2O.104 FE.62: 6 residues within 4Å: Chain M: T.12, G.14 Chain N: R.157, Y.162, Q.177, I.191 3 PLIP interactions: 1 interactions with chain N, 2 Ligand-Water interactions Metal complexes: N:Y.162, H2O.112, H2O.122 FE.71: 6 residues within 4Å: Chain O: T.12, G.14 Chain P: R.157, Y.162, Q.177, I.191 3 PLIP interactions: 1 interactions with chain P, 2 Ligand-Water interactions Metal complexes: P:Y.162, H2O.129, H2O.139 FE.81: 6 residues within 4Å: Chain Q: T.12, G.14 Chain R: R.157, Y.162, Q.177, I.191 3 PLIP interactions: 1 interactions with chain R, 2 Ligand-Water interactions Metal complexes: R:Y.162, H2O.147, H2O.156 FE.91: 6 residues within 4Å: Chain S: T.12, G.14 Chain T: R.157, Y.162, Q.177, I.191 3 PLIP interactions: 1 interactions with chain T, 2 Ligand-Water interactions Metal complexes: T:Y.162, H2O.164, H2O.174 FE.100: 6 residues within 4Å: Chain U: T.12, G.14 Chain V: R.157, Y.162, Q.177, I.191 3 PLIP interactions: 1 interactions with chain V, 2 Ligand-Water interactions Metal complexes: V:Y.162, H2O.182, H2O.191 FE.110: 6 residues within 4Å: Chain W: T.12, G.14 Chain X: R.157, Y.162, Q.177, I.191 3 PLIP interactions: 1 interactions with chain X, 2 Ligand-Water interactions Metal complexes: X:Y.162, H2O.199, H2O.208

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

CL.6: 2 residues within 4Å: Chain B: R.114, R.150 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain B: R.107, P.118, L.119 Ligand excluded by PLIP CL.28: 1 residues within 4Å: Chain F: R.83 Ligand excluded by PLIP CL.35: 2 residues within 4Å: Chain H: R.114, R.150 Ligand excluded by PLIP CL.38: 3 residues within 4Å: Chain H: R.107, P.118, L.119 Ligand excluded by PLIP CL.57: 1 residues within 4Å: Chain L: R.83 Ligand excluded by PLIP CL.64: 2 residues within 4Å: Chain N: R.114, R.150 Ligand excluded by PLIP CL.67: 3 residues within 4Å: Chain N: R.107, P.118, L.119 Ligand excluded by PLIP CL.86: 1 residues within 4Å: Chain R: R.83 Ligand excluded by PLIP CL.93: 2 residues within 4Å: Chain T: R.114, R.150 Ligand excluded by PLIP CL.96: 3 residues within 4Å: Chain T: R.107, P.118, L.119 Ligand excluded by PLIP CL.115: 1 residues within 4Å: Chain X: R.83 Ligand excluded by PLIP

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

BME.7: 2 residues within 4Å: Chain B: R.109, P.121 Ligand excluded by PLIP BME.8: 3 residues within 4Å: Chain B: H.234, F.235 Chain R: H.61 Ligand excluded by PLIP BME.15: 4 residues within 4Å: Chain D: T.233, H.234, F.235, E.236 Ligand excluded by PLIP BME.17: 3 residues within 4Å: Chain D: R.107, P.118, L.119 Ligand excluded by PLIP BME.21: 3 residues within 4Å: Chain E: P.164, R.167, E.168 Ligand excluded by PLIP BME.22: 4 residues within 4Å: Chain E: L.23, N.28, P.29 Chain F: F.67 Ligand excluded by PLIP BME.25: 3 residues within 4Å: Chain F: R.107, P.118, L.119 Ligand excluded by PLIP BME.26: 4 residues within 4Å: Chain F: T.21, P.22, D.23, K.193 Ligand excluded by PLIP BME.29: 4 residues within 4Å: Chain F: H.234, F.235 Chain V: H.61, S.138 Ligand excluded by PLIP BME.36: 2 residues within 4Å: Chain H: R.109, P.121 Ligand excluded by PLIP BME.37: 3 residues within 4Å: Chain H: H.234, F.235 Chain X: H.61 Ligand excluded by PLIP BME.44: 4 residues within 4Å: Chain J: T.233, H.234, F.235, E.236 Ligand excluded by PLIP BME.46: 3 residues within 4Å: Chain J: R.107, P.118, L.119 Ligand excluded by PLIP BME.50: 3 residues within 4Å: Chain K: P.164, R.167, E.168 Ligand excluded by PLIP BME.51: 4 residues within 4Å: Chain K: L.23, N.28, P.29 Chain L: F.67 Ligand excluded by PLIP BME.54: 3 residues within 4Å: Chain L: R.107, P.118, L.119 Ligand excluded by PLIP BME.55: 4 residues within 4Å: Chain L: T.21, P.22, D.23, K.193 Ligand excluded by PLIP BME.58: 4 residues within 4Å: Chain L: H.234, F.235 Chain P: H.61, S.138 Ligand excluded by PLIP BME.65: 2 residues within 4Å: Chain N: R.109, P.121 Ligand excluded by PLIP BME.66: 3 residues within 4Å: Chain F: H.61 Chain N: H.234, F.235 Ligand excluded by PLIP BME.73: 4 residues within 4Å: Chain P: T.233, H.234, F.235, E.236 Ligand excluded by PLIP BME.75: 3 residues within 4Å: Chain P: R.107, P.118, L.119 Ligand excluded by PLIP BME.79: 3 residues within 4Å: Chain Q: P.164, R.167, E.168 Ligand excluded by PLIP BME.80: 4 residues within 4Å: Chain Q: L.23, N.28, P.29 Chain R: F.67 Ligand excluded by PLIP BME.83: 3 residues within 4Å: Chain R: R.107, P.118, L.119 Ligand excluded by PLIP BME.84: 4 residues within 4Å: Chain R: T.21, P.22, D.23, K.193 Ligand excluded by PLIP BME.87: 4 residues within 4Å: Chain J: H.61, S.138 Chain R: H.234, F.235 Ligand excluded by PLIP BME.94: 2 residues within 4Å: Chain T: R.109, P.121 Ligand excluded by PLIP BME.95: 3 residues within 4Å: Chain L: H.61 Chain T: H.234, F.235 Ligand excluded by PLIP BME.102: 4 residues within 4Å: Chain V: T.233, H.234, F.235, E.236 Ligand excluded by PLIP BME.104: 3 residues within 4Å: Chain V: R.107, P.118, L.119 Ligand excluded by PLIP BME.108: 3 residues within 4Å: Chain W: P.164, R.167, E.168 Ligand excluded by PLIP BME.109: 4 residues within 4Å: Chain W: L.23, N.28, P.29 Chain X: F.67 Ligand excluded by PLIP BME.112: 3 residues within 4Å: Chain X: R.107, P.118, L.119 Ligand excluded by PLIP BME.113: 4 residues within 4Å: Chain X: T.21, P.22, D.23, K.193 Ligand excluded by PLIP BME.116: 4 residues within 4Å: Chain D: H.61, S.138 Chain X: H.234, F.235 Ligand excluded by PLIP

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

2011-04-27

Peptides

Protocatechuate 3,4-dioxygenase alpha chain: ACEGIKMOQSUW
Protocatechuate 3,4-dioxygenase beta chain: BDFHJLNPRTVX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
B

E
C

G
A

I
B

K
C

M
A

O
B

Q
C

S
A

U
B

W
C

B
M

D
N

F
O

H
M

J
N

L
O

N
M

P
N

R
O

T
M

V
N

X
O

Protocatechuate 3,4-dioxygenase alpha chain

Protocatechuate 3,4-dioxygenase beta chain

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