SMTL ID : 2buv.1

Crystal Structure Of Protocatechuate 3,4-Dioxygenase from Acinetobacter Sp. ADP1 Mutant R457S in Complex with Protocatechuate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-12-12-mer

Ligands

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

FE.1: 4 residues within 4Å: Chain B: Y.109, H.161, H.163 Ligands: DHB.2 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:Y.109, B:H.161, B:H.163 FE.3: 4 residues within 4Å: Chain D: Y.109, H.161, H.163 Ligands: DHB.4 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:Y.109, D:H.161, D:H.163 FE.5: 4 residues within 4Å: Chain F: Y.109, H.161, H.163 Ligands: DHB.6 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:Y.109, F:H.161, F:H.163 FE.7: 4 residues within 4Å: Chain H: Y.109, H.161, H.163 Ligands: DHB.8 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:Y.109, H:H.161, H:H.163 FE.9: 4 residues within 4Å: Chain J: Y.109, H.161, H.163 Ligands: DHB.10 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:Y.109, J:H.161, J:H.163 FE.11: 4 residues within 4Å: Chain L: Y.109, H.161, H.163 Ligands: DHB.12 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:Y.109, L:H.161, L:H.163 FE.13: 4 residues within 4Å: Chain N: Y.109, H.161, H.163 Ligands: DHB.14 3 PLIP interactions: 3 interactions with chain N Metal complexes: N:Y.109, N:H.161, N:H.163 FE.15: 4 residues within 4Å: Chain P: Y.109, H.161, H.163 Ligands: DHB.16 3 PLIP interactions: 3 interactions with chain P Metal complexes: P:Y.109, P:H.161, P:H.163 FE.17: 4 residues within 4Å: Chain R: Y.109, H.161, H.163 Ligands: DHB.18 3 PLIP interactions: 3 interactions with chain R Metal complexes: R:Y.109, R:H.161, R:H.163 FE.19: 4 residues within 4Å: Chain T: Y.109, H.161, H.163 Ligands: DHB.20 3 PLIP interactions: 3 interactions with chain T Metal complexes: T:Y.109, T:H.161, T:H.163 FE.21: 4 residues within 4Å: Chain V: Y.109, H.161, H.163 Ligands: DHB.22 3 PLIP interactions: 3 interactions with chain V Metal complexes: V:Y.109, V:H.161, V:H.163 FE.23: 4 residues within 4Å: Chain X: Y.109, H.161, H.163 Ligands: DHB.24 3 PLIP interactions: 3 interactions with chain X Metal complexes: X:Y.109, X:H.161, X:H.163

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

DHB.2: 11 residues within 4Å: Chain A: P.19, Y.20, R.142 Chain B: Y.109, Y.148, W.150, S.158, H.161, H.163, I.192 Ligands: FE.1 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:P.19, A:Y.20, B:Y.148, B:I.192 Water bridges: A:R.142, B:S.158 Hydrogen bonds: B:Y.148 pi-Stacking: B:W.150, B:W.150 DHB.4: 11 residues within 4Å: Chain C: P.19, Y.20, R.142 Chain D: Y.109, Y.148, W.150, S.158, H.161, H.163, I.192 Ligands: FE.3 8 PLIP interactions: 5 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:Y.148, D:I.192, C:P.19, C:Y.20 Water bridges: D:S.158, C:R.142 pi-Stacking: D:W.150, D:W.150 DHB.6: 11 residues within 4Å: Chain E: P.19, Y.20, R.142 Chain F: Y.109, Y.148, W.150, S.158, H.161, H.163, I.192 Ligands: FE.5 9 PLIP interactions: 6 interactions with chain F, 3 interactions with chain E Hydrophobic interactions: F:Y.148, F:I.192, E:P.19, E:Y.20 Water bridges: F:Y.25, F:S.158, E:R.142 pi-Stacking: F:W.150, F:W.150 DHB.8: 11 residues within 4Å: Chain G: P.19, Y.20, R.142 Chain H: Y.109, Y.148, W.150, S.158, H.161, H.163, I.192 Ligands: FE.7 9 PLIP interactions: 6 interactions with chain H, 3 interactions with chain G Hydrophobic interactions: H:Y.148, H:I.192, G:P.19, G:Y.20 Hydrogen bonds: H:Y.148 Water bridges: H:S.158, G:R.142 pi-Stacking: H:W.150, H:W.150 DHB.10: 11 residues within 4Å: Chain I: P.19, Y.20, R.142 Chain J: Y.109, Y.148, W.150, S.158, H.161, H.163, I.192 Ligands: FE.9 9 PLIP interactions: 6 interactions with chain J, 3 interactions with chain I Hydrophobic interactions: J:Y.148, J:I.192, I:P.19, I:Y.20 Water bridges: J:Y.25, J:S.158, I:R.142 pi-Stacking: J:W.150, J:W.150 DHB.12: 11 residues within 4Å: Chain K: P.19, Y.20, R.142 Chain L: Y.109, Y.148, W.150, S.158, H.161, H.163, I.192 Ligands: FE.11 10 PLIP interactions: 7 interactions with chain L, 3 interactions with chain K Hydrophobic interactions: L:Y.148, L:I.192, K:P.19, K:Y.20 Hydrogen bonds: L:Y.148 Water bridges: L:Y.25, L:S.158, K:R.142 pi-Stacking: L:W.150, L:W.150 DHB.14: 11 residues within 4Å: Chain M: P.19, Y.20, R.142 Chain N: Y.109, Y.148, W.150, S.158, H.161, H.163, I.192 Ligands: FE.13 8 PLIP interactions: 5 interactions with chain N, 3 interactions with chain M Hydrophobic interactions: N:Y.148, N:I.192, M:P.19, M:Y.20 Water bridges: N:S.158, M:R.142 pi-Stacking: N:W.150, N:W.150 DHB.16: 11 residues within 4Å: Chain O: P.19, Y.20, R.142 Chain P: Y.109, Y.148, W.150, S.158, H.161, H.163, I.192 Ligands: FE.15 11 PLIP interactions: 8 interactions with chain P, 3 interactions with chain O Hydrophobic interactions: P:Y.148, P:I.192, O:P.19, O:Y.20 Hydrogen bonds: P:Y.109, P:Y.148 Water bridges: P:S.158, P:H.163, O:R.142 pi-Stacking: P:W.150, P:W.150 DHB.18: 11 residues within 4Å: Chain Q: P.19, Y.20, R.142 Chain R: Y.109, Y.148, W.150, S.158, H.161, H.163, I.192 Ligands: FE.17 9 PLIP interactions: 6 interactions with chain R, 3 interactions with chain Q Hydrophobic interactions: R:Y.148, R:I.192, Q:P.19, Q:Y.20 Hydrogen bonds: R:Y.148 Water bridges: R:S.158, Q:R.142 pi-Stacking: R:W.150, R:W.150 DHB.20: 11 residues within 4Å: Chain S: P.19, Y.20, R.142 Chain T: Y.109, Y.148, W.150, S.158, H.161, H.163, I.192 Ligands: FE.19 9 PLIP interactions: 3 interactions with chain S, 6 interactions with chain T Hydrophobic interactions: S:P.19, S:Y.20, T:Y.148, T:I.192 Water bridges: S:R.142, T:Y.25, T:S.158 pi-Stacking: T:W.150, T:W.150 DHB.22: 11 residues within 4Å: Chain U: P.19, Y.20, R.142 Chain V: Y.109, Y.148, W.150, S.158, H.161, H.163, I.192 Ligands: FE.21 10 PLIP interactions: 7 interactions with chain V, 3 interactions with chain U Hydrophobic interactions: V:Y.148, V:I.192, U:P.19, U:Y.20 Hydrogen bonds: V:Y.148 Water bridges: V:Y.25, V:S.158, U:R.142 pi-Stacking: V:W.150, V:W.150 DHB.24: 11 residues within 4Å: Chain W: P.19, Y.20, R.142 Chain X: Y.109, Y.148, W.150, S.158, H.161, H.163, I.192 Ligands: FE.23 9 PLIP interactions: 6 interactions with chain X, 3 interactions with chain W Hydrophobic interactions: X:Y.148, X:I.192, W:P.19, W:Y.20 Water bridges: X:Y.25, X:S.158, W:R.142 pi-Stacking: X:W.150, X:W.150

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brown, C.K. et al., Biophysical Analyses of Designed and Selected Mutants of Protocatechuate 3,4-Dioxygenase. Annu.Rev.Microbiol. (2004)

Release Date

2006-09-04

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
A

E
A

G
A

I
A

K
A

M
A

O
A

Q
A

S
A

U
A

W
A

B
B

D
B

F
B

H
B

J
B

L
B

N
B

P
B

R
B

T
B

V
B

X
B

PROTOCATECHUATE 3,4-DIOXYGENASE ALPHA CHAIN

PROTOCATECHUATE 3,4-DIOXYGENASE BETA CHAIN

Related Entries With Identical Sequence