SMTL ID : 3pch.1

STRUCTURE OF PROTOCATECHUATE 3,4-DIOXYGENASE COMPLEXED WITH 3-CHLORO-4-HYDROXYBENZOATE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

hetero-oligomer

Ligands

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

FE.1: 5 residues within 4Å: Chain B: Y.108, Y.147, H.160, H.162 Ligands: CHB.8 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:Y.108, B:Y.147, B:H.160, B:H.162, H2O.8490 FE.2: 5 residues within 4Å: Chain D: Y.108, Y.147, H.160, H.162 Ligands: CHB.11 5 PLIP interactions: 1 Ligand-Water interactions, 4 interactions with chain D Metal complexes: H2O.8491, D:Y.108, D:Y.147, D:H.160, D:H.162 FE.3: 5 residues within 4Å: Ligands: CHB.14 Chain F: Y.108, Y.147, H.160, H.162 5 PLIP interactions: 1 Ligand-Water interactions, 4 interactions with chain F Metal complexes: H2O.8492, F:Y.108, F:Y.147, F:H.160, F:H.162 FE.4: 5 residues within 4Å: Chain H: Y.108, Y.147, H.160, H.162 Ligands: CHB.17 5 PLIP interactions: 4 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:Y.108, H:Y.147, H:H.160, H:H.162, H2O.8493 FE.5: 5 residues within 4Å: Chain J: Y.108, Y.147, H.160, H.162 Ligands: CHB.20 5 PLIP interactions: 4 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:Y.108, J:Y.147, J:H.160, J:H.162, H2O.8494 FE.6: 5 residues within 4Å: Chain L: Y.108, Y.147, H.160, H.162 Ligands: CHB.23 5 PLIP interactions: 1 Ligand-Water interactions, 4 interactions with chain L Metal complexes: H2O.8495, L:Y.108, L:Y.147, L:H.160, L:H.162 FE.25: 5 residues within 4Å: Ligands: CHB.32 Chain N: Y.108, Y.147, H.160, H.162 5 PLIP interactions: 1 Ligand-Water interactions, 4 interactions with chain N Metal complexes: H2O.5904, N:Y.108, N:Y.147, N:H.160, N:H.162 FE.26: 5 residues within 4Å: Chain P: Y.108, Y.147, H.160, H.162 Ligands: CHB.35 5 PLIP interactions: 4 interactions with chain P, 1 Ligand-Water interactions Metal complexes: P:Y.108, P:Y.147, P:H.160, P:H.162, H2O.5905 FE.27: 5 residues within 4Å: Chain R: Y.108, Y.147, H.160, H.162 Ligands: CHB.38 5 PLIP interactions: 4 interactions with chain R, 1 Ligand-Water interactions Metal complexes: R:Y.108, R:Y.147, R:H.160, R:H.162, H2O.5906 FE.28: 5 residues within 4Å: Chain T: Y.108, Y.147, H.160, H.162 Ligands: CHB.41 5 PLIP interactions: 1 Ligand-Water interactions, 4 interactions with chain T Metal complexes: H2O.5907, T:Y.108, T:Y.147, T:H.160, T:H.162 FE.29: 5 residues within 4Å: Ligands: CHB.44 Chain V: Y.108, Y.147, H.160, H.162 5 PLIP interactions: 1 Ligand-Water interactions, 4 interactions with chain V Metal complexes: H2O.5908, V:Y.108, V:Y.147, V:H.160, V:H.162 FE.30: 5 residues within 4Å: Chain X: Y.108, Y.147, H.160, H.162 Ligands: CHB.47 5 PLIP interactions: 4 interactions with chain X, 1 Ligand-Water interactions Metal complexes: X:Y.108, X:Y.147, X:H.160, X:H.162, H2O.5909

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

BME.7: 5 residues within 4Å: Chain B: H.61, C.129, L.130, Y.137, S.138 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.138 BME.10: 4 residues within 4Å: Chain D: H.61, C.129, L.130, S.138 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.138 BME.13: 4 residues within 4Å: Chain F: H.61, C.129, L.130, S.138 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:S.138 BME.16: 5 residues within 4Å: Chain H: H.61, C.129, L.130, Y.137, S.138 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:S.138 BME.19: 4 residues within 4Å: Chain J: H.61, C.129, L.130, S.138 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:S.138 BME.22: 5 residues within 4Å: Chain L: H.61, C.129, L.130, Y.137, S.138 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:S.138 BME.31: 5 residues within 4Å: Chain N: H.61, C.129, L.130, Y.137, S.138 1 PLIP interactions: 1 interactions with chain N Hydrogen bonds: N:S.138 BME.34: 4 residues within 4Å: Chain P: H.61, C.129, L.130, S.138 1 PLIP interactions: 1 interactions with chain P Hydrogen bonds: P:S.138 BME.37: 4 residues within 4Å: Chain R: H.61, C.129, L.130, S.138 1 PLIP interactions: 1 interactions with chain R Hydrogen bonds: R:S.138 BME.40: 5 residues within 4Å: Chain T: H.61, C.129, L.130, Y.137, S.138 1 PLIP interactions: 1 interactions with chain T Hydrogen bonds: T:S.138 BME.43: 4 residues within 4Å: Chain V: H.61, C.129, L.130, S.138 1 PLIP interactions: 1 interactions with chain V Hydrogen bonds: V:S.138 BME.46: 5 residues within 4Å: Chain X: H.61, C.129, L.130, Y.137, S.138 1 PLIP interactions: 1 interactions with chain X Hydrogen bonds: X:S.138

24 x CHB: 3-CHLORO-4-HYDROXYBENZOIC ACID(Non-covalent)

CHB.8: 14 residues within 4Å: Chain A: T.12, G.14, P.15, R.133 Chain B: Y.24, Y.108, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.1 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:P.15, B:Y.147, B:W.149, B:I.191 Hydrogen bonds: B:R.157 Salt bridges: A:R.133 Halogen bonds: B:Q.177 CHB.9: 4 residues within 4Å: Chain B: L.20, R.33 Chain F: P.22, I.28 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain F Hydrophobic interactions: B:L.20, F:P.22 pi-Cation interactions: B:R.33 Water bridges: F:R.33 CHB.11: 14 residues within 4Å: Chain C: T.12, G.14, P.15, R.133 Chain D: Y.24, Y.108, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.2 8 PLIP interactions: 2 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: C:P.15, D:Y.147, D:W.149, D:I.191 Hydrogen bonds: D:Y.24, D:R.157 Salt bridges: C:R.133 Halogen bonds: D:Q.177 CHB.12: 6 residues within 4Å: Chain B: L.20, P.22, I.28, R.33 Chain D: L.20, R.33 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:P.22, D:L.20 pi-Cation interactions: D:R.33 Water bridges: B:R.33 CHB.14: 14 residues within 4Å: Chain E: T.12, G.14, P.15, R.133 Ligands: FE.3 Chain F: Y.24, Y.108, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191 7 PLIP interactions: 2 interactions with chain E, 5 interactions with chain F Hydrophobic interactions: E:P.15, F:Y.147, F:W.149, F:I.191 Hydrogen bonds: F:R.157 Salt bridges: E:R.133 Halogen bonds: F:Q.177 CHB.15: 4 residues within 4Å: Chain D: P.22, I.28 Chain F: L.20, R.33 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain F Hydrophobic interactions: D:P.22, D:P.22, F:L.20 Water bridges: D:R.33 CHB.17: 14 residues within 4Å: Chain H: Y.24, Y.108, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.4 Chain G: T.12, G.14, P.15, R.133 10 PLIP interactions: 8 interactions with chain H, 2 interactions with chain G Hydrophobic interactions: H:Y.147, H:W.149, H:R.157, H:I.191, G:P.15 Hydrogen bonds: H:Y.108, H:R.157, H:H.162 Salt bridges: G:R.133 Halogen bonds: H:Q.177 CHB.18: 5 residues within 4Å: Chain H: L.20, R.33 Chain L: P.22, I.28, R.33 4 PLIP interactions: 2 interactions with chain H, 2 interactions with chain L Hydrophobic interactions: H:L.20, L:P.22, L:I.28 pi-Cation interactions: H:R.33 CHB.20: 14 residues within 4Å: Chain I: T.12, G.14, P.15, R.133 Chain J: Y.24, Y.108, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.5 10 PLIP interactions: 2 interactions with chain I, 8 interactions with chain J Hydrophobic interactions: I:P.15, J:Y.147, J:W.149, J:I.191 Hydrogen bonds: J:Y.24, J:Y.108, J:R.157, J:H.162 Salt bridges: I:R.133 Halogen bonds: J:Q.177 CHB.21: 4 residues within 4Å: Chain H: P.22, I.28 Chain J: L.20, R.33 5 PLIP interactions: 3 interactions with chain H, 2 interactions with chain J Hydrophobic interactions: H:P.22, H:P.22, J:L.20 pi-Cation interactions: J:R.33 Water bridges: H:R.33 CHB.23: 14 residues within 4Å: Chain K: T.12, G.14, P.15, R.133 Chain L: Y.24, Y.108, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.6 9 PLIP interactions: 2 interactions with chain K, 7 interactions with chain L Hydrophobic interactions: K:P.15, L:Y.147, L:W.149, L:R.157, L:I.191 Hydrogen bonds: L:R.157, L:H.162 Salt bridges: K:R.133 Halogen bonds: L:Q.177 CHB.24: 4 residues within 4Å: Chain J: L.20, P.22, I.28 Chain L: R.33 5 PLIP interactions: 4 interactions with chain J, 1 interactions with chain L Hydrophobic interactions: J:P.22, J:P.22, J:I.28 pi-Cation interactions: L:R.33 Water bridges: J:R.33 CHB.32: 14 residues within 4Å: Chain M: T.12, G.14, P.15, R.133 Ligands: FE.25 Chain N: Y.24, Y.108, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191 10 PLIP interactions: 2 interactions with chain M, 8 interactions with chain N Hydrophobic interactions: M:P.15, N:Y.147, N:W.149, N:I.191 Hydrogen bonds: N:Y.24, N:Y.147, N:R.157, N:H.162 Salt bridges: M:R.133 Halogen bonds: N:Q.177 CHB.33: 4 residues within 4Å: Chain R: P.22, I.28 Chain N: L.20, R.33 4 PLIP interactions: 2 interactions with chain R, 2 interactions with chain N Hydrophobic interactions: R:P.22, N:L.20 pi-Cation interactions: N:R.33 Water bridges: R:R.33 CHB.35: 14 residues within 4Å: Chain P: Y.24, Y.108, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.26 Chain O: T.12, G.14, P.15, R.133 9 PLIP interactions: 7 interactions with chain P, 2 interactions with chain O Hydrophobic interactions: P:Y.147, P:W.149, P:I.191, O:P.15 Hydrogen bonds: P:Y.147, P:R.157, P:H.162 Salt bridges: O:R.133 Halogen bonds: P:Q.177 CHB.36: 6 residues within 4Å: Chain P: L.20, R.33 Chain N: L.20, P.22, I.28, R.33 4 PLIP interactions: 2 interactions with chain P, 2 interactions with chain N Hydrophobic interactions: P:L.20, N:P.22 pi-Cation interactions: P:R.33 Water bridges: N:R.33 CHB.38: 14 residues within 4Å: Chain Q: T.12, G.14, P.15, R.133 Chain R: Y.24, Y.108, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.27 11 PLIP interactions: 2 interactions with chain Q, 9 interactions with chain R Hydrophobic interactions: Q:P.15, R:Y.147, R:W.149, R:I.191 Hydrogen bonds: R:Y.24, R:Y.108, R:Y.147, R:R.157, R:H.162 Salt bridges: Q:R.133 Halogen bonds: R:Q.177 CHB.39: 4 residues within 4Å: Chain P: P.22, I.28 Chain R: L.20, R.33 4 PLIP interactions: 3 interactions with chain P, 1 interactions with chain R Hydrophobic interactions: P:P.22, P:P.22, R:L.20 Water bridges: P:R.33 CHB.41: 14 residues within 4Å: Chain S: T.12, G.14, P.15, R.133 Chain T: Y.24, Y.108, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.28 11 PLIP interactions: 2 interactions with chain S, 9 interactions with chain T Hydrophobic interactions: S:P.15, T:Y.147, T:W.149, T:R.157, T:I.191 Hydrogen bonds: T:Y.24, T:Y.147, T:R.157, T:H.162 Salt bridges: S:R.133 Halogen bonds: T:Q.177 CHB.42: 5 residues within 4Å: Chain X: P.22, I.28, R.33 Chain T: L.20, R.33 3 PLIP interactions: 2 interactions with chain X, 1 interactions with chain T Hydrophobic interactions: X:P.22, X:I.28, T:L.20 CHB.44: 14 residues within 4Å: Chain U: T.12, G.14, P.15, R.133 Ligands: FE.29 Chain V: Y.24, Y.108, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191 9 PLIP interactions: 2 interactions with chain U, 7 interactions with chain V Hydrophobic interactions: U:P.15, V:Y.147, V:W.149, V:I.191 Hydrogen bonds: V:Y.147, V:R.157, V:H.162 Salt bridges: U:R.133 Halogen bonds: V:Q.177 CHB.45: 4 residues within 4Å: Chain T: P.22, I.28 Chain V: L.20, R.33 5 PLIP interactions: 3 interactions with chain T, 2 interactions with chain V Hydrophobic interactions: T:P.22, T:P.22, V:L.20 pi-Cation interactions: V:R.33 Water bridges: T:R.33 CHB.47: 14 residues within 4Å: Chain X: Y.24, Y.108, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.30 Chain W: T.12, G.14, P.15, R.133 12 PLIP interactions: 10 interactions with chain X, 2 interactions with chain W Hydrophobic interactions: X:Y.147, X:W.149, X:R.157, X:I.191, W:P.15 Hydrogen bonds: X:Y.24, X:Y.108, X:Y.147, X:R.157, X:H.162 Salt bridges: W:R.133 Halogen bonds: X:Q.177 CHB.48: 4 residues within 4Å: Chain X: R.33 Chain V: L.20, P.22, I.28 4 PLIP interactions: 4 interactions with chain V Hydrophobic interactions: V:P.22, V:P.22, V:I.28 Water bridges: V:R.33

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Orville, A.M. et al., Structures of competitive inhibitor complexes of protocatechuate 3,4-dioxygenase: multiple exogenous ligand binding orientations within the active site. Biochemistry (1997)

Release Date

1998-01-07

Peptides

PROTOCATECHUATE 3,4-DIOXYGENASE: ACEGIKMOQSUW
PROTOCATECHUATE 3,4-DIOXYGENASE: BDFHJLNPRTVX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
B

E
C

G
D

I
E

K
F

M
A

O
B

Q
C

S
D

U
E

W
F

B
M

D
N

F
O

H
P

J
Q

L
R

N
M

P
N

R
O

T
P

V
Q

X
R

PROTOCATECHUATE 3,4-DIOXYGENASE

PROTOCATECHUATE 3,4-DIOXYGENASE

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