SMTL ID : 9bb0.1

D-Dopachrome Tautomerase with 4-Hydroxyphenylpyruvate Bound in Catalytic Site at Atomic (0.98 Angstrom) Resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 0.99 Å

Oligo State

homo-21-mer

Ligands

49 x NA: SODIUM ION(Non-functional Binders)

NA.1: 5 residues within 4Å: Chain A: F.2, S.60, I.61, S.62 Chain M: R.98 Ligand excluded by PLIP NA.2: 4 residues within 4Å: Chain A: I.29, S.75, H.76, H.79 Ligand excluded by PLIP NA.5: 4 residues within 4Å: Chain B: F.2, S.60, I.61, S.62 Ligand excluded by PLIP NA.6: 4 residues within 4Å: Chain B: I.29, S.75, H.76, H.79 Ligand excluded by PLIP NA.7: 5 residues within 4Å: Chain B: Q.58, L.59, L.96, I.97, R.98 Ligand excluded by PLIP NA.8: 5 residues within 4Å: Chain B: D.35 Chain C: I.29, S.75, H.76, H.79 Ligand excluded by PLIP NA.9: 5 residues within 4Å: Chain C: F.2, L.3, N.38, V.39, T.40 Ligand excluded by PLIP NA.10: 5 residues within 4Å: Chain A: R.98 Chain D: F.2, S.60, I.61, S.62 Ligand excluded by PLIP NA.11: 4 residues within 4Å: Chain D: I.29, S.75, H.76, H.79 Ligand excluded by PLIP NA.14: 4 residues within 4Å: Chain E: F.2, S.60, I.61, S.62 Ligand excluded by PLIP NA.15: 4 residues within 4Å: Chain E: I.29, S.75, H.76, H.79 Ligand excluded by PLIP NA.16: 5 residues within 4Å: Chain E: Q.58, L.59, L.96, I.97, R.98 Ligand excluded by PLIP NA.17: 5 residues within 4Å: Chain E: D.35 Chain F: I.29, S.75, H.76, H.79 Ligand excluded by PLIP NA.18: 5 residues within 4Å: Chain F: F.2, L.3, N.38, V.39, T.40 Ligand excluded by PLIP NA.19: 4 residues within 4Å: Chain G: F.2, S.60, I.61, S.62 Ligand excluded by PLIP NA.20: 4 residues within 4Å: Chain G: I.29, S.75, H.76, H.79 Ligand excluded by PLIP NA.23: 4 residues within 4Å: Chain H: F.2, S.60, I.61, S.62 Ligand excluded by PLIP NA.24: 4 residues within 4Å: Chain H: I.29, S.75, H.76, H.79 Ligand excluded by PLIP NA.25: 5 residues within 4Å: Chain H: Q.58, L.59, L.96, I.97, R.98 Ligand excluded by PLIP NA.26: 5 residues within 4Å: Chain H: D.35 Chain I: I.29, S.75, H.76, H.79 Ligand excluded by PLIP NA.27: 5 residues within 4Å: Chain I: F.2, L.3, N.38, V.39, T.40 Ligand excluded by PLIP NA.28: 4 residues within 4Å: Chain J: F.2, S.60, I.61, S.62 Ligand excluded by PLIP NA.29: 4 residues within 4Å: Chain J: I.29, S.75, H.76, H.79 Ligand excluded by PLIP NA.32: 4 residues within 4Å: Chain K: F.2, S.60, I.61, S.62 Ligand excluded by PLIP NA.33: 4 residues within 4Å: Chain K: I.29, S.75, H.76, H.79 Ligand excluded by PLIP NA.34: 5 residues within 4Å: Chain K: Q.58, L.59, L.96, I.97, R.98 Ligand excluded by PLIP NA.35: 5 residues within 4Å: Chain K: D.35 Chain L: I.29, S.75, H.76, H.79 Ligand excluded by PLIP NA.36: 5 residues within 4Å: Chain L: F.2, L.3, N.38, V.39, T.40 Ligand excluded by PLIP NA.37: 5 residues within 4Å: Chain D: R.98 Chain M: F.2, S.60, I.61, S.62 Ligand excluded by PLIP NA.38: 4 residues within 4Å: Chain M: I.29, S.75, H.76, H.79 Ligand excluded by PLIP NA.41: 4 residues within 4Å: Chain N: F.2, S.60, I.61, S.62 Ligand excluded by PLIP NA.42: 4 residues within 4Å: Chain N: I.29, S.75, H.76, H.79 Ligand excluded by PLIP NA.43: 5 residues within 4Å: Chain N: Q.58, L.59, L.96, I.97, R.98 Ligand excluded by PLIP NA.44: 5 residues within 4Å: Chain N: D.35 Chain O: I.29, S.75, H.76, H.79 Ligand excluded by PLIP NA.45: 5 residues within 4Å: Chain O: F.2, L.3, N.38, V.39, T.40 Ligand excluded by PLIP NA.46: 4 residues within 4Å: Chain P: F.2, S.60, I.61, S.62 Ligand excluded by PLIP NA.47: 4 residues within 4Å: Chain P: I.29, S.75, H.76, H.79 Ligand excluded by PLIP NA.50: 4 residues within 4Å: Chain Q: F.2, S.60, I.61, S.62 Ligand excluded by PLIP NA.51: 4 residues within 4Å: Chain Q: I.29, S.75, H.76, H.79 Ligand excluded by PLIP NA.52: 5 residues within 4Å: Chain Q: Q.58, L.59, L.96, I.97, R.98 Ligand excluded by PLIP NA.53: 5 residues within 4Å: Chain Q: D.35 Chain R: I.29, S.75, H.76, H.79 Ligand excluded by PLIP NA.54: 5 residues within 4Å: Chain R: F.2, L.3, N.38, V.39, T.40 Ligand excluded by PLIP NA.55: 5 residues within 4Å: Chain G: R.98 Chain S: F.2, S.60, I.61, S.62 Ligand excluded by PLIP NA.56: 4 residues within 4Å: Chain S: I.29, S.75, H.76, H.79 Ligand excluded by PLIP NA.59: 4 residues within 4Å: Chain T: F.2, S.60, I.61, S.62 Ligand excluded by PLIP NA.60: 4 residues within 4Å: Chain T: I.29, S.75, H.76, H.79 Ligand excluded by PLIP NA.61: 5 residues within 4Å: Chain T: Q.58, L.59, L.96, I.97, R.98 Ligand excluded by PLIP NA.62: 5 residues within 4Å: Chain T: D.35 Chain U: I.29, S.75, H.76, H.79 Ligand excluded by PLIP NA.63: 5 residues within 4Å: Chain U: F.2, L.3, N.38, V.39, T.40 Ligand excluded by PLIP

7 x ENO: 3-(4-HYDROXY-PHENYL)PYRUVIC ACID(Non-covalent)

ENO.3: 10 residues within 4Å: Chain B: P.1, K.32, R.36, S.63, I.64, I.107, K.109, M.114 Chain C: S.28 Ligands: EN1.4 9 PLIP interactions: 1 interactions with chain C, 8 interactions with chain B Hydrogen bonds: C:S.28, B:P.1, B:R.36, B:I.64, B:K.109 Hydrophobic interactions: B:I.64, B:I.107, B:K.109 Salt bridges: B:K.32 ENO.12: 10 residues within 4Å: Chain E: P.1, K.32, R.36, S.63, I.64, I.107, K.109, M.114 Chain F: S.28 Ligands: EN1.13 9 PLIP interactions: 1 interactions with chain F, 8 interactions with chain E Hydrogen bonds: F:S.28, E:P.1, E:R.36, E:I.64, E:K.109 Hydrophobic interactions: E:I.64, E:I.107, E:K.109 Salt bridges: E:K.32 ENO.21: 10 residues within 4Å: Chain H: P.1, K.32, R.36, S.63, I.64, I.107, K.109, M.114 Chain I: S.28 Ligands: EN1.22 9 PLIP interactions: 8 interactions with chain H, 1 interactions with chain I Hydrophobic interactions: H:I.64, H:I.107, H:K.109 Hydrogen bonds: H:P.1, H:R.36, H:I.64, H:K.109, I:S.28 Salt bridges: H:K.32 ENO.30: 10 residues within 4Å: Chain K: P.1, K.32, R.36, S.63, I.64, I.107, K.109, M.114 Chain L: S.28 Ligands: EN1.31 9 PLIP interactions: 8 interactions with chain K, 1 interactions with chain L Hydrophobic interactions: K:I.64, K:I.107, K:K.109 Hydrogen bonds: K:P.1, K:R.36, K:I.64, K:K.109, L:S.28 Salt bridges: K:K.32 ENO.39: 10 residues within 4Å: Chain N: P.1, K.32, R.36, S.63, I.64, I.107, K.109, M.114 Chain O: S.28 Ligands: EN1.40 9 PLIP interactions: 8 interactions with chain N, 1 interactions with chain O Hydrophobic interactions: N:I.64, N:I.107, N:K.109 Hydrogen bonds: N:P.1, N:R.36, N:I.64, N:K.109, O:S.28 Salt bridges: N:K.32 ENO.48: 10 residues within 4Å: Chain Q: P.1, K.32, R.36, S.63, I.64, I.107, K.109, M.114 Chain R: S.28 Ligands: EN1.49 9 PLIP interactions: 8 interactions with chain Q, 1 interactions with chain R Hydrophobic interactions: Q:I.64, Q:I.107, Q:K.109 Hydrogen bonds: Q:P.1, Q:R.36, Q:I.64, Q:K.109, R:S.28 Salt bridges: Q:K.32 ENO.57: 10 residues within 4Å: Chain T: P.1, K.32, R.36, S.63, I.64, I.107, K.109, M.114 Chain U: S.28 Ligands: EN1.58 9 PLIP interactions: 8 interactions with chain T, 1 interactions with chain U Hydrophobic interactions: T:I.64, T:I.107, T:K.109 Hydrogen bonds: T:P.1, T:R.36, T:I.64, T:K.109, U:S.28 Salt bridges: T:K.32

7 x EN1: (2E)-2-hydroxy-3-(4-hydroxyphenyl)prop-2-enoic acid(Non-covalent)

EN1.4: 11 residues within 4Å: Chain B: P.1, F.2, R.36, S.62, S.63, I.64, I.107, K.109, M.114 Chain H: L.96 Ligands: ENO.3 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain H Hydrophobic interactions: B:I.107, B:I.107, B:K.109, H:L.96 Hydrogen bonds: B:P.1, B:P.1, B:I.64, B:K.109 Salt bridges: B:K.32 EN1.13: 10 residues within 4Å: Chain E: P.1, F.2, R.36, S.62, S.63, I.64, I.107, K.109, M.114 Ligands: ENO.12 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:I.107, E:I.107, E:K.109 Hydrogen bonds: E:P.1, E:P.1, E:I.64, E:K.109 Salt bridges: E:K.32 EN1.22: 11 residues within 4Å: Chain H: P.1, F.2, R.36, S.62, S.63, I.64, I.107, K.109, M.114 Chain Q: L.96 Ligands: ENO.21 9 PLIP interactions: 8 interactions with chain H, 1 interactions with chain Q Hydrophobic interactions: H:I.107, H:I.107, H:K.109, Q:L.96 Hydrogen bonds: H:P.1, H:P.1, H:I.64, H:K.109 Salt bridges: H:K.32 EN1.31: 11 residues within 4Å: Chain K: P.1, F.2, R.36, S.62, S.63, I.64, I.107, K.109, M.114 Chain N: L.96 Ligands: ENO.30 9 PLIP interactions: 8 interactions with chain K, 1 interactions with chain N Hydrophobic interactions: K:I.107, K:I.107, K:K.109, N:L.96 Hydrogen bonds: K:P.1, K:P.1, K:I.64, K:K.109 Salt bridges: K:K.32 EN1.40: 10 residues within 4Å: Chain N: P.1, F.2, R.36, S.62, S.63, I.64, I.107, K.109, M.114 Ligands: ENO.39 8 PLIP interactions: 8 interactions with chain N Hydrophobic interactions: N:I.107, N:I.107, N:K.109 Hydrogen bonds: N:P.1, N:P.1, N:I.64, N:K.109 Salt bridges: N:K.32 EN1.49: 11 residues within 4Å: Chain B: L.96 Chain Q: P.1, F.2, R.36, S.62, S.63, I.64, I.107, K.109, M.114 Ligands: ENO.48 9 PLIP interactions: 8 interactions with chain Q, 1 interactions with chain B Hydrophobic interactions: Q:I.107, Q:I.107, Q:K.109, B:L.96 Hydrogen bonds: Q:P.1, Q:P.1, Q:I.64, Q:K.109 Salt bridges: Q:K.32 EN1.58: 10 residues within 4Å: Chain T: P.1, F.2, R.36, S.62, S.63, I.64, I.107, K.109, M.114 Ligands: ENO.57 8 PLIP interactions: 8 interactions with chain T Hydrophobic interactions: T:I.107, T:I.107, T:K.109 Hydrogen bonds: T:P.1, T:P.1, T:I.64, T:K.109 Salt bridges: T:K.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Argueta, C. et al., D-Dopachrome Tautomerase with 4-Hydroxyphenylpyruvate Bound in Catalytic Site at Atomic (0.98 Angstrom) Resolution. To Be Published (2025)

Release Date

2025-03-12

Peptides

D-dopachrome decarboxylase: ABCDEFGHIJKLMNOPQRSTU

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

C
CCC

D
AAA

E
BBB

F
CCC

G
AAA

H
BBB

I
CCC

J
AAA

K
BBB

L
CCC

M
AAA

N
BBB

O
CCC

P
AAA

Q
BBB

R
CCC

S
AAA

T
BBB

U
CCC

D-dopachrome decarboxylase

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