SMTL ID : 6hx2.1

The structure of Dps from Listeria innocua soaked with Cobalt

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-12-mer

Ligands

90 x CO: COBALT (II) ION(Non-covalent)(Non-functional Binders)

CO.1: 4 residues within 4Å: Chain A: D.58, E.62 Chain D: H.31, W.32 6 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: A:D.58, A:D.58, A:E.62, D:H.31, H2O.4, H2O.23 CO.2: 2 residues within 4Å: Chain A: H.15 Ligands: CO.8 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.15, H2O.2, H2O.5, H2O.6, H2O.6 CO.3: 1 residues within 4Å: Chain A: T.41 No protein-ligand interaction detected (PLIP) CO.4: 4 residues within 4Å: Chain A: H.37 Chain K: D.96, L.150 Ligands: CO.10 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.37, H2O.7, H2O.76, H2O.79, H2O.81 CO.5: 2 residues within 4Å: Chain A: D.96 Chain L: H.37 2 PLIP interactions: 1 interactions with chain L, 1 interactions with chain A Metal complexes: L:H.37, A:D.96 CO.6: 2 residues within 4Å: Chain A: E.55, D.58 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.55, H2O.1, H2O.6, H2O.7, H2O.7 CO.7: 2 residues within 4Å: Chain A: H.37 Chain K: H.37 No protein-ligand interaction detected (PLIP) CO.8: 2 residues within 4Å: Chain A: E.11 Ligands: CO.2 No protein-ligand interaction detected (PLIP) CO.9: 5 residues within 4Å: Chain A: D.130, A.134 Chain F: D.130 Ligands: CO.18, CO.43 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.130, A:D.130, H2O.4, H2O.5 CO.10: 3 residues within 4Å: Chain A: H.37 Chain K: D.96 Ligands: CO.4 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain K, 1 Ligand-Water interactions Metal complexes: A:H.37, K:D.96, H2O.76 CO.11: 4 residues within 4Å: Chain B: D.58, E.62 Chain E: H.31, W.32 6 PLIP interactions: 1 interactions with chain E, 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: E:H.31, B:D.58, B:D.58, B:E.62, H2O.10, H2O.33 CO.12: 3 residues within 4Å: Chain B: M.1, H.15, N.81 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:H.15, H2O.8, H2O.9, H2O.13, H2O.14 CO.13: 2 residues within 4Å: Chain B: D.96 Chain D: H.37 5 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: D:H.37, B:D.96, H2O.8, H2O.24, H2O.25 CO.14: 3 residues within 4Å: Chain B: H.37 Chain C: D.96, L.150 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.37, H2O.14, H2O.15, H2O.19 CO.15: 1 residues within 4Å: Chain B: D.130 No protein-ligand interaction detected (PLIP) CO.16: 6 residues within 4Å: Chain B: N.38, T.41 Chain C: N.38, T.41 Chain D: N.38, T.41 No protein-ligand interaction detected (PLIP) CO.17: 2 residues within 4Å: Chain B: E.55, D.58 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.55, H2O.9, H2O.9, H2O.13, H2O.15 CO.18: 5 residues within 4Å: Chain A: D.130 Chain B: D.130 Chain F: D.130 Ligands: CO.9, CO.43 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.130, H2O.11 CO.19: 5 residues within 4Å: Chain C: D.58, E.62 Chain I: H.31, W.32, H.43 6 PLIP interactions: 3 interactions with chain C, 1 interactions with chain I, 2 Ligand-Water interactions Metal complexes: C:D.58, C:D.58, C:E.62, I:H.31, H2O.61, H2O.62 CO.20: 3 residues within 4Å: Chain C: H.37 Chain D: D.96, L.150 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:H.37, H2O.23, H2O.24, H2O.27, H2O.28 CO.21: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CO.22: 2 residues within 4Å: Chain C: H.15 Ligands: CO.25 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:H.15, H2O.16, H2O.20, H2O.20, H2O.20 CO.23: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CO.24: 2 residues within 4Å: Chain C: E.55, D.58 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.55, C:E.55, H2O.16, H2O.20, H2O.75 CO.25: 2 residues within 4Å: Chain C: E.11 Ligands: CO.22 No protein-ligand interaction detected (PLIP) CO.26: 5 residues within 4Å: Chain C: D.130 Chain E: D.130 Chain J: D.130 Ligands: CO.27, CO.40 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.130, H2O.19 CO.27: 3 residues within 4Å: Chain J: D.130 Ligands: CO.26, CO.40 3 PLIP interactions: 2 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:D.130, J:D.130, H2O.70 CO.28: 4 residues within 4Å: Chain A: H.31, W.32 Chain D: D.58, E.62 6 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: D:D.58, D:D.58, D:E.62, A:H.31, H2O.2, H2O.24 CO.29: 2 residues within 4Å: Chain D: M.1, H.15 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:M.1, D:H.15, H2O.24, H2O.27, H2O.28 CO.30: 2 residues within 4Å: Chain D: E.118, D.121 No protein-ligand interaction detected (PLIP) CO.31: 2 residues within 4Å: Chain D: G.124, D.126 No protein-ligand interaction detected (PLIP) CO.32: 2 residues within 4Å: Chain D: E.55, D.58 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.55, D:E.55, H2O.23, H2O.28 CO.33: 2 residues within 4Å: Chain D: M.1, K.2 No protein-ligand interaction detected (PLIP) CO.34: 4 residues within 4Å: Chain B: H.31, W.32 Chain E: D.58, E.62 6 PLIP interactions: 3 interactions with chain E, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: E:D.58, E:D.58, E:E.62, B:H.31, H2O.9, H2O.32 CO.35: 2 residues within 4Å: Chain E: H.15, N.81 6 PLIP interactions: 1 interactions with chain E, 5 Ligand-Water interactions Metal complexes: E:H.15, H2O.32, H2O.35, H2O.36, H2O.36, H2O.37 CO.36: 2 residues within 4Å: Chain E: H.37 Chain F: D.96 5 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: E:H.37, F:D.96, H2O.34, H2O.39, H2O.43 CO.37: 6 residues within 4Å: Chain E: N.38, T.41 Chain F: N.38, T.41 Chain G: N.38, T.41 No protein-ligand interaction detected (PLIP) CO.38: 3 residues within 4Å: Chain B: D.47 Chain E: E.55, D.58 No protein-ligand interaction detected (PLIP) CO.39: 2 residues within 4Å: Chain E: G.124, D.126 No protein-ligand interaction detected (PLIP) CO.40: 5 residues within 4Å: Chain C: D.130 Chain E: D.130 Chain J: D.130 Ligands: CO.26, CO.27 3 PLIP interactions: 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.130, E:D.130, H2O.34 CO.41: 4 residues within 4Å: Chain F: D.58, E.62 Chain L: H.31, W.32 5 PLIP interactions: 1 interactions with chain L, 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: L:H.31, F:D.58, F:E.62, H2O.39, H2O.84 CO.42: 2 residues within 4Å: Chain F: H.15 Ligands: CO.45 5 PLIP interactions: 1 interactions with chain F, 4 Ligand-Water interactions Metal complexes: F:H.15, H2O.41, H2O.43, H2O.44, H2O.44 CO.43: 4 residues within 4Å: Chain B: D.130 Chain F: D.130 Ligands: CO.9, CO.18 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.130, F:D.130, H2O.39, H2O.41 CO.44: 2 residues within 4Å: Chain F: E.55, D.58 5 PLIP interactions: 1 interactions with chain F, 4 Ligand-Water interactions Metal complexes: F:E.55, H2O.38, H2O.42, H2O.43, H2O.45 CO.45: 2 residues within 4Å: Chain F: N.81 Ligands: CO.42 No protein-ligand interaction detected (PLIP) CO.46: 4 residues within 4Å: Chain G: D.58, E.62 Chain J: H.31, W.32 6 PLIP interactions: 3 interactions with chain G, 1 interactions with chain J, 2 Ligand-Water interactions Metal complexes: G:D.58, G:D.58, G:E.62, J:H.31, H2O.49, H2O.68 CO.47: 2 residues within 4Å: Chain G: H.15 Ligands: CO.53 5 PLIP interactions: 1 interactions with chain G, 4 Ligand-Water interactions Metal complexes: G:H.15, H2O.47, H2O.50, H2O.51, H2O.51 CO.48: 1 residues within 4Å: Chain G: T.41 No protein-ligand interaction detected (PLIP) CO.49: 4 residues within 4Å: Chain E: D.96, L.150 Chain G: H.37 Ligands: CO.55 5 PLIP interactions: 1 interactions with chain G, 4 Ligand-Water interactions Metal complexes: G:H.37, H2O.31, H2O.34, H2O.36, H2O.52 CO.50: 2 residues within 4Å: Chain F: H.37 Chain G: D.96 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain G Metal complexes: F:H.37, G:D.96 CO.51: 2 residues within 4Å: Chain G: E.55, D.58 5 PLIP interactions: 1 interactions with chain G, 4 Ligand-Water interactions Metal complexes: G:E.55, H2O.46, H2O.51, H2O.52, H2O.52 CO.52: 2 residues within 4Å: Chain E: H.37 Chain G: H.37 No protein-ligand interaction detected (PLIP) CO.53: 2 residues within 4Å: Chain G: E.11 Ligands: CO.47 No protein-ligand interaction detected (PLIP) CO.54: 5 residues within 4Å: Chain G: D.130, A.134 Chain L: D.130 Ligands: CO.63, CO.88 4 PLIP interactions: 2 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:D.130, G:D.130, H2O.49, H2O.50 CO.55: 3 residues within 4Å: Chain E: D.96 Chain G: H.37 Ligands: CO.49 3 PLIP interactions: 1 interactions with chain E, 1 interactions with chain G, 1 Ligand-Water interactions Metal complexes: E:D.96, G:H.37, H2O.31 CO.56: 4 residues within 4Å: Chain H: D.58, E.62 Chain K: H.31, W.32 6 PLIP interactions: 3 interactions with chain H, 1 interactions with chain K, 2 Ligand-Water interactions Metal complexes: H:D.58, H:D.58, H:E.62, K:H.31, H2O.55, H2O.78 CO.57: 3 residues within 4Å: Chain H: M.1, H.15, N.81 5 PLIP interactions: 1 interactions with chain H, 4 Ligand-Water interactions Metal complexes: H:H.15, H2O.53, H2O.54, H2O.58, H2O.59 CO.58: 2 residues within 4Å: Chain H: D.96 Chain J: H.37 5 PLIP interactions: 1 interactions with chain H, 1 interactions with chain J, 3 Ligand-Water interactions Metal complexes: H:D.96, J:H.37, H2O.53, H2O.69, H2O.70 CO.59: 3 residues within 4Å: Chain H: H.37 Chain I: D.96, L.150 4 PLIP interactions: 1 interactions with chain H, 3 Ligand-Water interactions Metal complexes: H:H.37, H2O.59, H2O.60, H2O.64 CO.60: 1 residues within 4Å: Chain H: D.130 No protein-ligand interaction detected (PLIP) CO.61: 6 residues within 4Å: Chain H: N.38, T.41 Chain I: N.38, T.41 Chain J: N.38, T.41 No protein-ligand interaction detected (PLIP) CO.62: 2 residues within 4Å: Chain H: E.55, D.58 5 PLIP interactions: 1 interactions with chain H, 4 Ligand-Water interactions Metal complexes: H:E.55, H2O.54, H2O.54, H2O.58, H2O.60 CO.63: 5 residues within 4Å: Chain G: D.130 Chain H: D.130 Chain L: D.130 Ligands: CO.54, CO.88 2 PLIP interactions: 1 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:D.130, H2O.56 CO.64: 5 residues within 4Å: Chain C: H.31, W.32, H.43 Chain I: D.58, E.62 6 PLIP interactions: 3 interactions with chain I, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: I:D.58, I:D.58, I:E.62, C:H.31, H2O.16, H2O.17 CO.65: 3 residues within 4Å: Chain I: H.37 Chain J: D.96, L.150 5 PLIP interactions: 1 interactions with chain I, 4 Ligand-Water interactions Metal complexes: I:H.37, H2O.68, H2O.69, H2O.72, H2O.73 CO.66: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CO.67: 2 residues within 4Å: Chain I: H.15 Ligands: CO.70 5 PLIP interactions: 1 interactions with chain I, 4 Ligand-Water interactions Metal complexes: I:H.15, H2O.61, H2O.65, H2O.65, H2O.65 CO.68: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CO.69: 2 residues within 4Å: Chain I: E.55, D.58 5 PLIP interactions: 2 interactions with chain I, 3 Ligand-Water interactions Metal complexes: I:E.55, I:E.55, H2O.30, H2O.61, H2O.65 CO.70: 2 residues within 4Å: Chain I: E.11 Ligands: CO.67 No protein-ligand interaction detected (PLIP) CO.71: 5 residues within 4Å: Chain D: D.130 Chain I: D.130 Chain K: D.130 Ligands: CO.72, CO.85 2 PLIP interactions: 1 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:D.130, H2O.64 CO.72: 3 residues within 4Å: Chain D: D.130 Ligands: CO.71, CO.85 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.130, D:D.130, H2O.25 CO.73: 4 residues within 4Å: Chain G: H.31, W.32 Chain J: D.58, E.62 6 PLIP interactions: 1 interactions with chain G, 3 interactions with chain J, 2 Ligand-Water interactions Metal complexes: G:H.31, J:D.58, J:D.58, J:E.62, H2O.47, H2O.69 CO.74: 2 residues within 4Å: Chain J: M.1, H.15 5 PLIP interactions: 2 interactions with chain J, 3 Ligand-Water interactions Metal complexes: J:M.1, J:H.15, H2O.69, H2O.72, H2O.73 CO.75: 2 residues within 4Å: Chain J: E.118, D.121 No protein-ligand interaction detected (PLIP) CO.76: 2 residues within 4Å: Chain J: G.124, D.126 No protein-ligand interaction detected (PLIP) CO.77: 2 residues within 4Å: Chain J: E.55, D.58 4 PLIP interactions: 2 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:E.55, J:E.55, H2O.68, H2O.73 CO.78: 2 residues within 4Å: Chain J: M.1, K.2 No protein-ligand interaction detected (PLIP) CO.79: 4 residues within 4Å: Chain H: H.31, W.32 Chain K: D.58, E.62 6 PLIP interactions: 3 interactions with chain K, 1 interactions with chain H, 2 Ligand-Water interactions Metal complexes: K:D.58, K:D.58, K:E.62, H:H.31, H2O.54, H2O.77 CO.80: 2 residues within 4Å: Chain K: H.15, N.81 6 PLIP interactions: 1 interactions with chain K, 5 Ligand-Water interactions Metal complexes: K:H.15, H2O.77, H2O.80, H2O.81, H2O.81, H2O.82 CO.81: 2 residues within 4Å: Chain K: H.37 Chain L: D.96 5 PLIP interactions: 1 interactions with chain K, 1 interactions with chain L, 3 Ligand-Water interactions Metal complexes: K:H.37, L:D.96, H2O.79, H2O.84, H2O.88 CO.82: 6 residues within 4Å: Chain A: N.38, T.41 Chain K: N.38, T.41 Chain L: N.38, T.41 No protein-ligand interaction detected (PLIP) CO.83: 3 residues within 4Å: Chain H: D.47 Chain K: E.55, D.58 No protein-ligand interaction detected (PLIP) CO.84: 2 residues within 4Å: Chain K: G.124, D.126 No protein-ligand interaction detected (PLIP) CO.85: 5 residues within 4Å: Chain D: D.130 Chain I: D.130 Chain K: D.130 Ligands: CO.71, CO.72 3 PLIP interactions: 2 interactions with chain K, 1 Ligand-Water interactions Metal complexes: K:D.130, K:D.130, H2O.79 CO.86: 4 residues within 4Å: Chain F: H.31, W.32 Chain L: D.58, E.62 5 PLIP interactions: 2 interactions with chain L, 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: L:D.58, L:E.62, F:H.31, H2O.39, H2O.84 CO.87: 2 residues within 4Å: Chain L: H.15 Ligands: CO.90 5 PLIP interactions: 1 interactions with chain L, 4 Ligand-Water interactions Metal complexes: L:H.15, H2O.86, H2O.88, H2O.89, H2O.89 CO.88: 4 residues within 4Å: Chain H: D.130 Chain L: D.130 Ligands: CO.54, CO.63 4 PLIP interactions: 2 interactions with chain L, 2 Ligand-Water interactions Metal complexes: L:D.130, L:D.130, H2O.84, H2O.86 CO.89: 2 residues within 4Å: Chain L: E.55, D.58 5 PLIP interactions: 1 interactions with chain L, 4 Ligand-Water interactions Metal complexes: L:E.55, H2O.83, H2O.87, H2O.88, H2O.90 CO.90: 2 residues within 4Å: Chain L: N.81 Ligands: CO.87 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zeth, K. et al., Metal Positions and Translocation Pathways of the Dodecameric Ferritin-like Protein Dps. Inorg.Chem. (2019)

Release Date

2019-09-04

Peptides

DNA protection during starvation protein: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
A

H
B

I
C

J
D

K
E

L
F

DNA protection during starvation protein

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