SMTL ID : 1eoa.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

hetero-12-12-mer

Ligands

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

FE.1: 6 residues within 4Å: Chain B: Y.109, H.161, H.163 Ligands: CYN.2, CYN.3, CYN.4 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:Y.109, B:H.161, B:H.163 FE.5: 6 residues within 4Å: Chain D: Y.109, H.161, H.163 Ligands: CYN.6, CYN.7, CYN.8 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:Y.109, D:H.161, D:H.163 FE.9: 6 residues within 4Å: Chain F: Y.109, H.161, H.163 Ligands: CYN.10, CYN.11, CYN.12 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:Y.109, F:H.161, F:H.163 FE.13: 6 residues within 4Å: Chain H: Y.109, H.161, H.163 Ligands: CYN.14, CYN.15, CYN.16 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:Y.109, H:H.161, H:H.163 FE.17: 6 residues within 4Å: Chain J: Y.109, H.161, H.163 Ligands: CYN.18, CYN.19, CYN.20 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:Y.109, J:H.161, J:H.163 FE.21: 6 residues within 4Å: Chain L: Y.109, H.161, H.163 Ligands: CYN.22, CYN.23, CYN.24 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:Y.109, L:H.161, L:H.163 FE.25: 6 residues within 4Å: Chain N: Y.109, H.161, H.163 Ligands: CYN.26, CYN.27, CYN.28 3 PLIP interactions: 3 interactions with chain N Metal complexes: N:Y.109, N:H.161, N:H.163 FE.29: 6 residues within 4Å: Chain P: Y.109, H.161, H.163 Ligands: CYN.30, CYN.31, CYN.32 3 PLIP interactions: 3 interactions with chain P Metal complexes: P:Y.109, P:H.161, P:H.163 FE.33: 6 residues within 4Å: Chain R: Y.109, H.161, H.163 Ligands: CYN.34, CYN.35, CYN.36 3 PLIP interactions: 3 interactions with chain R Metal complexes: R:Y.109, R:H.161, R:H.163 FE.37: 6 residues within 4Å: Chain T: Y.109, H.161, H.163 Ligands: CYN.38, CYN.39, CYN.40 3 PLIP interactions: 3 interactions with chain T Metal complexes: T:Y.109, T:H.161, T:H.163 FE.41: 6 residues within 4Å: Chain V: Y.109, H.161, H.163 Ligands: CYN.42, CYN.43, CYN.44 3 PLIP interactions: 3 interactions with chain V Metal complexes: V:Y.109, V:H.161, V:H.163 FE.45: 6 residues within 4Å: Chain X: Y.109, H.161, H.163 Ligands: CYN.46, CYN.47, CYN.48 3 PLIP interactions: 3 interactions with chain X Metal complexes: X:Y.109, X:H.161, X:H.163

36 x CYN: CYANIDE ION(Non-covalent)

CYN.2: 8 residues within 4Å: Chain B: Y.109, R.158, H.161, H.163, Q.178 Ligands: FE.1, CYN.3, CYN.4 Ligand excluded by PLIP CYN.3: 8 residues within 4Å: Chain B: Y.109, Y.148, R.158, H.161, H.163 Ligands: FE.1, CYN.2, CYN.4 Ligand excluded by PLIP CYN.4: 8 residues within 4Å: Chain A: G.18, P.19, Y.20 Chain B: Y.109, H.163 Ligands: FE.1, CYN.2, CYN.3 Ligand excluded by PLIP CYN.6: 8 residues within 4Å: Chain D: Y.109, R.158, H.161, H.163, Q.178 Ligands: FE.5, CYN.7, CYN.8 Ligand excluded by PLIP CYN.7: 8 residues within 4Å: Chain D: Y.109, Y.148, R.158, H.161, H.163 Ligands: FE.5, CYN.6, CYN.8 Ligand excluded by PLIP CYN.8: 8 residues within 4Å: Chain C: G.18, P.19, Y.20 Chain D: Y.109, H.163 Ligands: FE.5, CYN.6, CYN.7 Ligand excluded by PLIP CYN.10: 8 residues within 4Å: Chain F: Y.109, R.158, H.161, H.163, Q.178 Ligands: FE.9, CYN.11, CYN.12 Ligand excluded by PLIP CYN.11: 8 residues within 4Å: Chain F: Y.109, Y.148, R.158, H.161, H.163 Ligands: FE.9, CYN.10, CYN.12 Ligand excluded by PLIP CYN.12: 8 residues within 4Å: Chain E: G.18, P.19, Y.20 Chain F: Y.109, H.163 Ligands: FE.9, CYN.10, CYN.11 Ligand excluded by PLIP CYN.14: 8 residues within 4Å: Chain H: Y.109, R.158, H.161, H.163, Q.178 Ligands: FE.13, CYN.15, CYN.16 Ligand excluded by PLIP CYN.15: 8 residues within 4Å: Chain H: Y.109, Y.148, R.158, H.161, H.163 Ligands: FE.13, CYN.14, CYN.16 Ligand excluded by PLIP CYN.16: 8 residues within 4Å: Chain G: G.18, P.19, Y.20 Chain H: Y.109, H.163 Ligands: FE.13, CYN.14, CYN.15 Ligand excluded by PLIP CYN.18: 8 residues within 4Å: Chain J: Y.109, R.158, H.161, H.163, Q.178 Ligands: FE.17, CYN.19, CYN.20 Ligand excluded by PLIP CYN.19: 8 residues within 4Å: Chain J: Y.109, Y.148, R.158, H.161, H.163 Ligands: FE.17, CYN.18, CYN.20 Ligand excluded by PLIP CYN.20: 8 residues within 4Å: Chain I: G.18, P.19, Y.20 Chain J: Y.109, H.163 Ligands: FE.17, CYN.18, CYN.19 Ligand excluded by PLIP CYN.22: 8 residues within 4Å: Chain L: Y.109, R.158, H.161, H.163, Q.178 Ligands: FE.21, CYN.23, CYN.24 Ligand excluded by PLIP CYN.23: 8 residues within 4Å: Chain L: Y.109, Y.148, R.158, H.161, H.163 Ligands: FE.21, CYN.22, CYN.24 Ligand excluded by PLIP CYN.24: 8 residues within 4Å: Chain K: G.18, P.19, Y.20 Chain L: Y.109, H.163 Ligands: FE.21, CYN.22, CYN.23 Ligand excluded by PLIP CYN.26: 8 residues within 4Å: Chain N: Y.109, R.158, H.161, H.163, Q.178 Ligands: FE.25, CYN.27, CYN.28 Ligand excluded by PLIP CYN.27: 8 residues within 4Å: Chain N: Y.109, Y.148, R.158, H.161, H.163 Ligands: FE.25, CYN.26, CYN.28 Ligand excluded by PLIP CYN.28: 8 residues within 4Å: Chain M: G.18, P.19, Y.20 Chain N: Y.109, H.163 Ligands: FE.25, CYN.26, CYN.27 Ligand excluded by PLIP CYN.30: 8 residues within 4Å: Chain P: Y.109, R.158, H.161, H.163, Q.178 Ligands: FE.29, CYN.31, CYN.32 Ligand excluded by PLIP CYN.31: 8 residues within 4Å: Chain P: Y.109, Y.148, R.158, H.161, H.163 Ligands: FE.29, CYN.30, CYN.32 Ligand excluded by PLIP CYN.32: 8 residues within 4Å: Chain O: G.18, P.19, Y.20 Chain P: Y.109, H.163 Ligands: FE.29, CYN.30, CYN.31 Ligand excluded by PLIP CYN.34: 8 residues within 4Å: Chain R: Y.109, R.158, H.161, H.163, Q.178 Ligands: FE.33, CYN.35, CYN.36 Ligand excluded by PLIP CYN.35: 8 residues within 4Å: Chain R: Y.109, Y.148, R.158, H.161, H.163 Ligands: FE.33, CYN.34, CYN.36 Ligand excluded by PLIP CYN.36: 8 residues within 4Å: Chain Q: G.18, P.19, Y.20 Chain R: Y.109, H.163 Ligands: FE.33, CYN.34, CYN.35 Ligand excluded by PLIP CYN.38: 8 residues within 4Å: Chain T: Y.109, R.158, H.161, H.163, Q.178 Ligands: FE.37, CYN.39, CYN.40 Ligand excluded by PLIP CYN.39: 8 residues within 4Å: Chain T: Y.109, Y.148, R.158, H.161, H.163 Ligands: FE.37, CYN.38, CYN.40 Ligand excluded by PLIP CYN.40: 8 residues within 4Å: Chain S: G.18, P.19, Y.20 Chain T: Y.109, H.163 Ligands: FE.37, CYN.38, CYN.39 Ligand excluded by PLIP CYN.42: 8 residues within 4Å: Chain V: Y.109, R.158, H.161, H.163, Q.178 Ligands: FE.41, CYN.43, CYN.44 Ligand excluded by PLIP CYN.43: 8 residues within 4Å: Chain V: Y.109, Y.148, R.158, H.161, H.163 Ligands: FE.41, CYN.42, CYN.44 Ligand excluded by PLIP CYN.44: 8 residues within 4Å: Chain U: G.18, P.19, Y.20 Chain V: Y.109, H.163 Ligands: FE.41, CYN.42, CYN.43 Ligand excluded by PLIP CYN.46: 8 residues within 4Å: Chain X: Y.109, R.158, H.161, H.163, Q.178 Ligands: FE.45, CYN.47, CYN.48 Ligand excluded by PLIP CYN.47: 8 residues within 4Å: Chain X: Y.109, Y.148, R.158, H.161, H.163 Ligands: FE.45, CYN.46, CYN.48 Ligand excluded by PLIP CYN.48: 8 residues within 4Å: Chain W: G.18, P.19, Y.20 Chain X: Y.109, H.163 Ligands: FE.45, CYN.46, CYN.47 Ligand excluded by PLIP

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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