SMTL ID : 6the.1

Crystal structure of core domain of four-domain heme-cupredoxin-Cu nitrite reductase from Bradyrhizobium sp. ORS 375

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.87 Å

Oligo State

homo-trimer

Ligands

6 x CU: COPPER (II) ION(Non-covalent)

CU.1: 5 residues within 4Å: Chain A: I.83, H.84, C.125, H.133, M.138 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.84, A:C.125, A:H.133 CU.2: 5 residues within 4Å: Chain A: D.87, H.89, H.124 Chain B: H.230, H.281 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:H.89, A:H.124, B:H.281, H2O.1 CU.21: 5 residues within 4Å: Chain B: I.83, H.84, C.125, H.133, M.138 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.84, B:C.125, B:H.133 CU.22: 5 residues within 4Å: Chain B: D.87, H.89, H.124 Chain C: H.230, H.281 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: B:H.89, B:H.124, C:H.281, H2O.3 CU.41: 5 residues within 4Å: Chain C: I.83, H.84, C.125, H.133, M.138 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.84, C:C.125, C:H.133 CU.42: 5 residues within 4Å: Chain A: H.230, H.281 Chain C: D.87, H.89, H.124 4 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: A:H.281, C:H.89, C:H.124, H2O.5

9 x YB: YTTERBIUM (III) ION(Non-functional Binders)(Non-covalent)

YB.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) YB.4: 1 residues within 4Å: Chain A: T.275 No protein-ligand interaction detected (PLIP) YB.5: 3 residues within 4Å: Chain A: L.62, R.63 Ligands: 9JE.17 No protein-ligand interaction detected (PLIP) YB.23: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) YB.24: 1 residues within 4Å: Chain B: T.275 No protein-ligand interaction detected (PLIP) YB.25: 3 residues within 4Å: Chain B: L.62, R.63 Ligands: 9JE.37 No protein-ligand interaction detected (PLIP) YB.43: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) YB.44: 1 residues within 4Å: Chain C: T.275 No protein-ligand interaction detected (PLIP) YB.45: 3 residues within 4Å: Chain C: L.62, R.63 Ligands: 9JE.57 No protein-ligand interaction detected (PLIP)

12 x ER3: ERBIUM (III) ION(Non-covalent)(Non-functional Binders)

ER3.6: 1 residues within 4Å: Chain A: R.30 No protein-ligand interaction detected (PLIP) ER3.7: 2 residues within 4Å: Ligands: TB.10, YT3.11 No protein-ligand interaction detected (PLIP) ER3.8: 2 residues within 4Å: Chain A: G.49, F.178 No protein-ligand interaction detected (PLIP) ER3.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ER3.26: 1 residues within 4Å: Chain B: R.30 No protein-ligand interaction detected (PLIP) ER3.27: 2 residues within 4Å: Ligands: TB.30, YT3.31 No protein-ligand interaction detected (PLIP) ER3.28: 2 residues within 4Å: Chain B: G.49, F.178 No protein-ligand interaction detected (PLIP) ER3.29: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ER3.46: 1 residues within 4Å: Chain C: R.30 No protein-ligand interaction detected (PLIP) ER3.47: 2 residues within 4Å: Ligands: TB.50, YT3.51 No protein-ligand interaction detected (PLIP) ER3.48: 2 residues within 4Å: Chain C: G.49, F.178 No protein-ligand interaction detected (PLIP) ER3.49: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

3 x TB: TERBIUM(III) ION(Non-covalent)

TB.10: 3 residues within 4Å: Chain A: D.154 Ligands: ER3.7, YT3.11 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.154 TB.30: 3 residues within 4Å: Chain B: D.154 Ligands: ER3.27, YT3.31 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.154 TB.50: 3 residues within 4Å: Chain C: D.154 Ligands: ER3.47, YT3.51 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.154

6 x YT3: YTTRIUM (III) ION(Non-covalent)

YT3.11: 3 residues within 4Å: Chain A: D.154 Ligands: ER3.7, TB.10 No protein-ligand interaction detected (PLIP) YT3.12: 3 residues within 4Å: Chain A: D.16, V.17, P.18 No protein-ligand interaction detected (PLIP) YT3.31: 3 residues within 4Å: Chain B: D.154 Ligands: ER3.27, TB.30 No protein-ligand interaction detected (PLIP) YT3.32: 3 residues within 4Å: Chain B: D.16, V.17, P.18 No protein-ligand interaction detected (PLIP) YT3.51: 3 residues within 4Å: Chain C: D.154 Ligands: ER3.47, TB.50 No protein-ligand interaction detected (PLIP) YT3.52: 3 residues within 4Å: Chain C: D.16, V.17, P.18 No protein-ligand interaction detected (PLIP)

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.13: 3 residues within 4Å: Chain A: R.12, N.54, P.60 Ligand excluded by PLIP CL.33: 3 residues within 4Å: Chain B: R.12, N.54, P.60 Ligand excluded by PLIP CL.53: 3 residues within 4Å: Chain C: R.12, N.54, P.60 Ligand excluded by PLIP

21 x 9JE: pentane-1,5-diol(Non-covalent)

9JE.14: 2 residues within 4Å: Chain A: A.77, D.79 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.77 9JE.15: 3 residues within 4Å: Chain A: T.28, R.30, E.71 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.28 9JE.16: 2 residues within 4Å: Chain A: I.83, P.128 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.83 9JE.17: 4 residues within 4Å: Chain A: P.18, D.32, L.61 Ligands: YB.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.32, A:D.32, A:D.32, A:L.61 9JE.18: 2 residues within 4Å: Chain A: R.30, E.108 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.30, A:R.30, A:E.108 9JE.19: 3 residues within 4Å: Chain A: D.15, H.204, P.205 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.15 9JE.20: 1 residues within 4Å: Chain A: E.177 No protein-ligand interaction detected (PLIP) 9JE.34: 2 residues within 4Å: Chain B: A.77, D.79 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.77 9JE.35: 3 residues within 4Å: Chain B: T.28, R.30, E.71 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.28 9JE.36: 2 residues within 4Å: Chain B: I.83, P.128 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.83 9JE.37: 4 residues within 4Å: Chain B: P.18, D.32, L.61 Ligands: YB.25 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.32, B:D.32, B:L.61 9JE.38: 2 residues within 4Å: Chain B: R.30, E.108 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.30, B:R.30, B:E.108 9JE.39: 3 residues within 4Å: Chain B: D.15, H.204, P.205 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.15 9JE.40: 1 residues within 4Å: Chain B: E.177 No protein-ligand interaction detected (PLIP) 9JE.54: 2 residues within 4Å: Chain C: A.77, D.79 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:A.77 9JE.55: 3 residues within 4Å: Chain C: T.28, R.30, E.71 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.28 9JE.56: 2 residues within 4Å: Chain C: I.83, P.128 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.83 9JE.57: 4 residues within 4Å: Chain C: P.18, D.32, L.61 Ligands: YB.45 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.32, C:D.32, C:L.61 9JE.58: 2 residues within 4Å: Chain C: R.30, E.108 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.30, C:R.30, C:E.108 9JE.59: 3 residues within 4Å: Chain C: D.15, H.204, P.205 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.15 9JE.60: 1 residues within 4Å: Chain C: E.177 No protein-ligand interaction detected (PLIP)

Links

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Citation

Sasaki, D. et al., Reverse protein engineering of a novel 4-domain copper nitrite reductase reveals functional regulation by protein-protein interaction. Febs J. (2021)

Release Date

2020-04-22

Peptides

Copper-containing nitrite reductase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Copper-containing nitrite reductase