SMTL ID : 1ykn.1

Protocatechuate 3,4-dioxygenase Y408E mutant bound to DHB

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.06 Å

Oligo State

hetero-12-12-mer

Ligands

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

FE.1: 5 residues within 4Å: Chain B: E.108, Y.147, H.160, H.162 Ligands: DHB.2 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:Y.147, B:H.160, B:H.162, H2O.9 FE.3: 5 residues within 4Å: Chain D: E.108, Y.147, H.160, H.162 Ligands: DHB.4 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:Y.147, D:H.160, D:H.162, H2O.19 FE.5: 5 residues within 4Å: Chain F: E.108, Y.147, H.160, H.162 Ligands: DHB.6 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:Y.147, F:H.160, F:H.162, H2O.29 FE.7: 4 residues within 4Å: Chain H: Y.147, H.160, H.162 Ligands: DHB.8 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:Y.147, H:H.160, H:H.162, H2O.38 FE.9: 5 residues within 4Å: Chain J: E.108, Y.147, H.160, H.162 Ligands: DHB.10 4 PLIP interactions: 3 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:Y.147, J:H.160, J:H.162, H2O.48 FE.11: 5 residues within 4Å: Chain L: E.108, Y.147, H.160, H.162 Ligands: DHB.12 4 PLIP interactions: 3 interactions with chain L, 1 Ligand-Water interactions Metal complexes: L:Y.147, L:H.160, L:H.162, H2O.58 FE.13: 5 residues within 4Å: Chain N: E.108, Y.147, H.160, H.162 Ligands: DHB.14 4 PLIP interactions: 3 interactions with chain N, 1 Ligand-Water interactions Metal complexes: N:Y.147, N:H.160, N:H.162, H2O.67 FE.15: 5 residues within 4Å: Chain P: E.108, Y.147, H.160, H.162 Ligands: DHB.16 4 PLIP interactions: 3 interactions with chain P, 1 Ligand-Water interactions Metal complexes: P:Y.147, P:H.160, P:H.162, H2O.77 FE.17: 5 residues within 4Å: Chain R: E.108, Y.147, H.160, H.162 Ligands: DHB.18 4 PLIP interactions: 3 interactions with chain R, 1 Ligand-Water interactions Metal complexes: R:Y.147, R:H.160, R:H.162, H2O.87 FE.19: 4 residues within 4Å: Chain T: Y.147, H.160, H.162 Ligands: DHB.20 4 PLIP interactions: 3 interactions with chain T, 1 Ligand-Water interactions Metal complexes: T:Y.147, T:H.160, T:H.162, H2O.96 FE.21: 5 residues within 4Å: Chain V: E.108, Y.147, H.160, H.162 Ligands: DHB.22 4 PLIP interactions: 3 interactions with chain V, 1 Ligand-Water interactions Metal complexes: V:Y.147, V:H.160, V:H.162, H2O.106 FE.23: 5 residues within 4Å: Chain X: E.108, Y.147, H.160, H.162 Ligands: DHB.24 4 PLIP interactions: 3 interactions with chain X, 1 Ligand-Water interactions Metal complexes: X:Y.147, X:H.160, X:H.162, H2O.116

12 x DHB: 3,4-DIHYDROXYBENZOIC ACID(Non-covalent)

DHB.2: 13 residues within 4Å: Chain A: T.12, G.14, P.15, R.133 Chain B: Y.24, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.1 11 PLIP interactions: 5 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:T.12, A:P.15, B:Y.147, B:W.149, B:I.191 Hydrogen bonds: A:T.12, A:G.134, B:Y.147, B:R.157, B:Q.177 Salt bridges: A:R.133 DHB.4: 13 residues within 4Å: Chain C: T.12, G.14, P.15, R.133 Chain D: Y.24, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.3 12 PLIP interactions: 4 interactions with chain C, 8 interactions with chain D Hydrophobic interactions: C:T.12, C:P.15, D:Y.147, D:W.149, D:R.157, D:I.191 Hydrogen bonds: C:G.134, D:Y.24, D:Y.147, D:R.157, D:Q.177 Salt bridges: C:R.133 DHB.6: 14 residues within 4Å: Chain E: T.12, G.14, P.15, R.133, G.134 Chain F: Y.24, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.5 11 PLIP interactions: 7 interactions with chain F, 4 interactions with chain E Hydrophobic interactions: F:Y.147, F:W.149, F:R.157, F:I.191, E:T.12, E:P.15 Hydrogen bonds: F:R.157, F:Q.177, E:G.134 Water bridges: F:T.26 Salt bridges: E:R.133 DHB.8: 13 residues within 4Å: Chain G: T.12, G.14, P.15, R.133 Chain H: Y.24, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.7 12 PLIP interactions: 7 interactions with chain H, 5 interactions with chain G Hydrophobic interactions: H:Y.147, H:W.149, H:R.157, H:I.191, G:T.12, G:P.15 Hydrogen bonds: H:Y.147, H:R.157, H:Q.177, G:T.12, G:G.134 Salt bridges: G:R.133 DHB.10: 14 residues within 4Å: Chain I: T.12, G.14, P.15, R.133, G.134 Chain J: Y.24, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.9 10 PLIP interactions: 4 interactions with chain I, 6 interactions with chain J Hydrophobic interactions: I:T.12, I:P.15, J:Y.147, J:W.149, J:I.191 Hydrogen bonds: I:G.134, J:Y.24, J:R.157, J:Q.177 Salt bridges: I:R.133 DHB.12: 13 residues within 4Å: Chain K: T.12, G.14, P.15, R.133 Chain L: Y.24, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.11 11 PLIP interactions: 4 interactions with chain K, 7 interactions with chain L Hydrophobic interactions: K:T.12, K:P.15, L:Y.147, L:W.149, L:R.157, L:I.191 Hydrogen bonds: K:G.134, L:R.157, L:Q.177 Salt bridges: K:R.133 Water bridges: L:T.26 DHB.14: 13 residues within 4Å: Chain M: T.12, G.14, P.15, R.133 Chain N: Y.24, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.13 12 PLIP interactions: 7 interactions with chain N, 5 interactions with chain M Hydrophobic interactions: N:Y.147, N:W.149, N:I.191, M:T.12, M:P.15 Hydrogen bonds: N:Y.24, N:R.157, N:Q.177, M:T.12, M:G.134 Water bridges: N:T.26 Salt bridges: M:R.133 DHB.16: 13 residues within 4Å: Chain O: T.12, G.14, P.15, R.133 Chain P: Y.24, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.15 13 PLIP interactions: 9 interactions with chain P, 4 interactions with chain O Hydrophobic interactions: P:Y.147, P:W.149, P:R.157, P:I.191, O:T.12, O:P.15 Hydrogen bonds: P:R.157, P:H.160, P:Q.177, O:G.134 Water bridges: P:T.26, P:T.26 Salt bridges: O:R.133 DHB.18: 14 residues within 4Å: Chain Q: T.12, G.14, P.15, R.133, G.134 Chain R: Y.24, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.17 11 PLIP interactions: 4 interactions with chain Q, 7 interactions with chain R Hydrophobic interactions: Q:T.12, Q:P.15, R:Y.147, R:W.149, R:R.157, R:I.191 Hydrogen bonds: Q:G.134, R:Y.24, R:R.157, R:Q.177 Salt bridges: Q:R.133 DHB.20: 13 residues within 4Å: Chain S: T.12, G.14, P.15, R.133 Chain T: Y.24, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.19 13 PLIP interactions: 5 interactions with chain S, 8 interactions with chain T Hydrophobic interactions: S:T.12, S:P.15, T:Y.147, T:W.149, T:R.157, T:I.191 Hydrogen bonds: S:T.12, S:G.134, T:Y.24, T:R.157, T:Q.177 Salt bridges: S:R.133 Water bridges: T:T.26 DHB.22: 14 residues within 4Å: Chain U: T.12, G.14, P.15, R.133, G.134 Chain V: Y.24, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.21 11 PLIP interactions: 4 interactions with chain U, 7 interactions with chain V Hydrophobic interactions: U:T.12, U:P.15, V:Y.147, V:W.149, V:I.191 Hydrogen bonds: U:G.134, V:Y.147, V:R.157, V:Q.177 Salt bridges: U:R.133 Water bridges: V:T.26 DHB.24: 13 residues within 4Å: Chain W: T.12, G.14, P.15, R.133 Chain X: Y.24, Y.147, W.149, R.157, H.160, H.162, Q.177, I.191 Ligands: FE.23 12 PLIP interactions: 4 interactions with chain W, 8 interactions with chain X Hydrophobic interactions: W:T.12, W:P.15, X:Y.147, X:W.149, X:R.157, X:I.191 Hydrogen bonds: W:G.134, X:Y.24, X:Y.147, X:R.157, X:Q.177 Salt bridges: W:R.133

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Valley, M.P. et al., Roles of the equatorial tyrosyl iron ligand of protocatechuate 3,4-dioxygenase in catalysis. Biochemistry (2005)

Release Date

2005-08-16

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
C

E
E

G
G

I
I

K
K

M
A

O
C

Q
E

S
G

U
I

W
K

B
B

D
D

F
F

H
H

J
J

L
L

N
B

P
D

R
F

T
H

V
J

X
L

Protocatechuate 3,4-dioxygenase alpha chain

Protocatechuate 3,4-dioxygenase beta chain

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