SMTL ID : 1eob.1

CRYSTAL STRUCTURE OF ACINETOBACTER SP. ADP1 PROTOCATECHUATE 3,4-DIOXYGENASE IN COMPLEX WITH 3,4-DIHYDROXYBENZOATE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-12-12-mer

Ligands

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

FE.1: 5 residues within 4Å: Chain B: Y.109, R.158, 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: 5 residues within 4Å: Chain D: Y.109, R.158, 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: 5 residues within 4Å: Chain F: Y.109, R.158, 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: 5 residues within 4Å: Chain H: Y.109, R.158, 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: 5 residues within 4Å: Chain J: Y.109, R.158, 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: 5 residues within 4Å: Chain L: Y.109, R.158, 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: 5 residues within 4Å: Chain N: Y.109, R.158, 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: 5 residues within 4Å: Chain P: Y.109, R.158, 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: 5 residues within 4Å: Chain R: Y.109, R.158, 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: 5 residues within 4Å: Chain T: Y.109, R.158, 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: 5 residues within 4Å: Chain V: Y.109, R.158, 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: 5 residues within 4Å: Chain X: Y.109, R.158, 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: 14 residues within 4Å: Chain A: T.16, G.18, P.19, R.142 Chain B: Y.25, Y.109, Y.148, W.150, R.158, H.161, H.163, Q.178, I.192 Ligands: FE.1 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:P.19, B:Y.148, B:W.150, B:R.158, B:I.192 Water bridges: A:R.142 Hydrogen bonds: B:R.158, B:Q.178 DHB.4: 14 residues within 4Å: Chain C: T.16, G.18, P.19, R.142 Chain D: Y.25, Y.109, Y.148, W.150, R.158, H.161, H.163, Q.178, I.192 Ligands: FE.3 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:Y.148, D:W.150, D:R.158, D:I.192, C:P.19 Hydrogen bonds: D:R.158, D:Q.178 Water bridges: C:R.142 DHB.6: 14 residues within 4Å: Chain E: T.16, G.18, P.19, R.142 Chain F: Y.25, Y.109, Y.148, W.150, R.158, H.161, H.163, Q.178, I.192 Ligands: FE.5 10 PLIP interactions: 8 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: F:Y.148, F:W.150, F:R.158, F:I.192, E:P.19 Hydrogen bonds: F:Y.25, F:R.158, F:Q.178 Water bridges: F:T.27, E:R.142 DHB.8: 14 residues within 4Å: Chain G: T.16, G.18, P.19, R.142 Chain H: Y.25, Y.109, Y.148, W.150, R.158, H.161, H.163, Q.178, I.192 Ligands: FE.7 10 PLIP interactions: 8 interactions with chain H, 2 interactions with chain G Hydrophobic interactions: H:Y.148, H:W.150, H:R.158, H:I.192, G:P.19 Hydrogen bonds: H:Y.25, H:R.158, H:Q.178 Water bridges: H:T.27, G:R.142 DHB.10: 14 residues within 4Å: Chain I: T.16, G.18, P.19, R.142 Chain J: Y.25, Y.109, Y.148, W.150, R.158, H.161, H.163, Q.178, I.192 Ligands: FE.9 8 PLIP interactions: 6 interactions with chain J, 2 interactions with chain I Hydrophobic interactions: J:Y.148, J:W.150, J:R.158, J:I.192, I:P.19 Hydrogen bonds: J:R.158, J:Q.178 Water bridges: I:R.142 DHB.12: 14 residues within 4Å: Chain K: T.16, G.18, P.19, R.142 Chain L: Y.25, Y.109, Y.148, W.150, R.158, H.161, H.163, Q.178, I.192 Ligands: FE.11 10 PLIP interactions: 8 interactions with chain L, 2 interactions with chain K Hydrophobic interactions: L:Y.148, L:W.150, L:R.158, L:I.192, K:P.19 Hydrogen bonds: L:Y.25, L:R.158, L:Q.178 Water bridges: L:T.27, K:R.142 DHB.14: 14 residues within 4Å: Chain M: T.16, G.18, P.19, R.142 Chain N: Y.25, Y.109, Y.148, W.150, R.158, H.161, H.163, Q.178, I.192 Ligands: FE.13 8 PLIP interactions: 6 interactions with chain N, 2 interactions with chain M Hydrophobic interactions: N:Y.148, N:W.150, N:R.158, N:I.192, M:P.19 Hydrogen bonds: N:R.158, N:Q.178 Water bridges: M:R.142 DHB.16: 14 residues within 4Å: Chain O: T.16, G.18, P.19, R.142 Chain P: Y.25, Y.109, Y.148, W.150, R.158, H.161, H.163, Q.178, I.192 Ligands: FE.15 13 PLIP interactions: 11 interactions with chain P, 2 interactions with chain O Hydrophobic interactions: P:Y.148, P:W.150, P:R.158, P:I.192, O:P.19 Hydrogen bonds: P:Y.25, P:Y.109, P:R.158, P:H.161, P:Q.178, P:Q.178 Water bridges: P:T.27, O:R.142 DHB.18: 14 residues within 4Å: Chain Q: T.16, G.18, P.19, R.142 Chain R: Y.25, Y.109, Y.148, W.150, R.158, H.161, H.163, Q.178, I.192 Ligands: FE.17 9 PLIP interactions: 7 interactions with chain R, 2 interactions with chain Q Hydrophobic interactions: R:Y.148, R:W.150, R:R.158, R:I.192, Q:P.19 Hydrogen bonds: R:R.158, R:Q.178 Water bridges: R:T.27, Q:R.142 DHB.20: 14 residues within 4Å: Chain S: T.16, G.18, P.19, R.142 Chain T: Y.25, Y.109, Y.148, W.150, R.158, H.161, H.163, Q.178, I.192 Ligands: FE.19 9 PLIP interactions: 7 interactions with chain T, 2 interactions with chain S Hydrophobic interactions: T:Y.148, T:W.150, T:R.158, T:I.192, S:P.19 Hydrogen bonds: T:Y.25, T:R.158, T:Q.178 Water bridges: S:R.142 DHB.22: 14 residues within 4Å: Chain U: T.16, G.18, P.19, R.142 Chain V: Y.25, Y.109, Y.148, W.150, R.158, H.161, H.163, Q.178, I.192 Ligands: FE.21 9 PLIP interactions: 7 interactions with chain V, 2 interactions with chain U Hydrophobic interactions: V:Y.148, V:W.150, V:R.158, V:I.192, U:P.19 Hydrogen bonds: V:Y.25, V:R.158, V:Q.178 Water bridges: U:R.142 DHB.24: 14 residues within 4Å: Chain W: T.16, G.18, P.19, R.142 Chain X: Y.25, Y.109, Y.148, W.150, R.158, H.161, H.163, Q.178, I.192 Ligands: FE.23 9 PLIP interactions: 2 interactions with chain W, 7 interactions with chain X Hydrophobic interactions: W:P.19, X:Y.148, X:W.150, X:R.158, X:I.192 Water bridges: W:R.142, X:T.27 Hydrogen bonds: X:R.158, X:Q.178

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vetting, M.W. et al., Structure of Acinetobacter strain ADP1 protocatechuate 3, 4-dioxygenase at 2.2 A resolution: implications for the mechanism of an intradiol dioxygenase. Biochemistry (2000)

Release Date

2000-08-09

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

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