SMTL ID : 6nw5.1

Crystal structure of TmPep1050 aminopeptidase with its metal cofactors

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-12-mer

Ligands

12 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: H.60, D.168, D.169, E.197, D.220 Ligands: CO.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.60, A:D.168, A:D.220, A:D.220, H2O.11 ZN.9: 6 residues within 4Å: Chain B: H.60, D.168, D.169, E.197, D.220 Ligands: CO.10 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.60, B:D.168, B:D.220, B:D.220, H2O.26 ZN.19: 6 residues within 4Å: Chain C: H.60, D.168, D.169, E.197, D.220 Ligands: CO.20 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.60, C:D.168, C:D.220, C:D.220, H2O.39 ZN.26: 7 residues within 4Å: Chain D: H.60, D.168, D.169, E.197, D.220 Ligands: CO.27, OH.34 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Ligand interactions Metal complexes: D:H.60, D:D.168, D:D.220, D:D.220, OH.34 ZN.35: 6 residues within 4Å: Chain E: H.60, D.168, D.169, E.197, D.220 Ligands: CO.36 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.60, E:D.168, E:D.220, E:D.220, H2O.68 ZN.43: 6 residues within 4Å: Chain F: H.60, D.168, D.169, E.197, D.220 Ligands: CO.44 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.60, F:D.168, F:D.220, F:D.220, H2O.83 ZN.53: 6 residues within 4Å: Chain G: H.60, D.168, D.169, E.197, D.220 Ligands: CO.54 5 PLIP interactions: 4 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:H.60, G:D.168, G:D.220, G:D.220, H2O.96 ZN.60: 7 residues within 4Å: Chain H: H.60, D.168, D.169, E.197, D.220 Ligands: CO.61, OH.68 5 PLIP interactions: 4 interactions with chain H, 1 Ligand-Ligand interactions Metal complexes: H:H.60, H:D.168, H:D.220, H:D.220, OH.68 ZN.69: 6 residues within 4Å: Chain I: H.60, D.168, D.169, E.197, D.220 Ligands: CO.70 5 PLIP interactions: 4 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:H.60, I:D.168, I:D.220, I:D.220, H2O.124 ZN.77: 6 residues within 4Å: Chain J: H.60, D.168, D.169, E.197, D.220 Ligands: CO.78 5 PLIP interactions: 4 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:H.60, J:D.168, J:D.220, J:D.220, H2O.139 ZN.87: 6 residues within 4Å: Chain K: H.60, D.168, D.169, E.197, D.220 Ligands: CO.88 5 PLIP interactions: 4 interactions with chain K, 1 Ligand-Water interactions Metal complexes: K:H.60, K:D.168, K:D.220, K:D.220, H2O.153 ZN.94: 7 residues within 4Å: Chain L: H.60, D.168, D.169, E.197, D.220 Ligands: CO.95, OH.102 5 PLIP interactions: 4 interactions with chain L, 1 Ligand-Ligand interactions Metal complexes: L:H.60, L:D.168, L:D.220, L:D.220, OH.102

12 x CO: COBALT (II) ION(Non-covalent)

CO.2: 4 residues within 4Å: Chain A: D.168, E.198, H.307 Ligands: ZN.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.168, A:E.198, A:E.198, A:H.307, H2O.11 CO.10: 4 residues within 4Å: Chain B: D.168, E.198, H.307 Ligands: ZN.9 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.168, B:E.198, B:E.198, B:H.307, H2O.26 CO.20: 4 residues within 4Å: Chain C: D.168, E.198, H.307 Ligands: ZN.19 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.168, C:E.198, C:E.198, C:H.307, H2O.39 CO.27: 5 residues within 4Å: Chain D: D.168, E.198, H.307 Ligands: ZN.26, OH.34 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Ligand interactions Metal complexes: D:D.168, D:E.198, D:E.198, D:H.307, OH.34 CO.36: 4 residues within 4Å: Chain E: D.168, E.198, H.307 Ligands: ZN.35 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.168, E:E.198, E:E.198, E:H.307, H2O.68 CO.44: 4 residues within 4Å: Chain F: D.168, E.198, H.307 Ligands: ZN.43 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.168, F:E.198, F:E.198, F:H.307, H2O.83 CO.54: 4 residues within 4Å: Chain G: D.168, E.198, H.307 Ligands: ZN.53 5 PLIP interactions: 4 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.168, G:E.198, G:E.198, G:H.307, H2O.96 CO.61: 5 residues within 4Å: Chain H: D.168, E.198, H.307 Ligands: ZN.60, OH.68 5 PLIP interactions: 4 interactions with chain H, 1 Ligand-Ligand interactions Metal complexes: H:D.168, H:E.198, H:E.198, H:H.307, OH.68 CO.70: 4 residues within 4Å: Chain I: D.168, E.198, H.307 Ligands: ZN.69 5 PLIP interactions: 4 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:D.168, I:E.198, I:E.198, I:H.307, H2O.124 CO.78: 4 residues within 4Å: Chain J: D.168, E.198, H.307 Ligands: ZN.77 5 PLIP interactions: 4 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:D.168, J:E.198, J:E.198, J:H.307, H2O.139 CO.88: 4 residues within 4Å: Chain K: D.168, E.198, H.307 Ligands: ZN.87 5 PLIP interactions: 4 interactions with chain K, 1 Ligand-Water interactions Metal complexes: K:D.168, K:E.198, K:E.198, K:H.307, H2O.153 CO.95: 5 residues within 4Å: Chain L: D.168, E.198, H.307 Ligands: ZN.94, OH.102 5 PLIP interactions: 4 interactions with chain L, 1 Ligand-Ligand interactions Metal complexes: L:D.168, L:E.198, L:E.198, L:H.307, OH.102

75 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 5 residues within 4Å: Chain A: K.2, R.6, F.155, V.156, E.157 Ligand excluded by PLIP SO4.4: 4 residues within 4Å: Chain A: G.40 Chain E: S.254, K.255, R.256 Ligand excluded by PLIP SO4.5: 4 residues within 4Å: Chain A: V.71, D.72, D.73, R.136 Ligand excluded by PLIP SO4.6: 1 residues within 4Å: Chain A: R.327 Ligand excluded by PLIP SO4.7: 2 residues within 4Å: Chain A: K.271, Y.272 Ligand excluded by PLIP SO4.8: 4 residues within 4Å: Chain A: M.1, K.2, E.3, L.4 Ligand excluded by PLIP SO4.11: 3 residues within 4Å: Chain B: S.254, K.255, R.256 Ligand excluded by PLIP SO4.12: 5 residues within 4Å: Chain B: K.2, R.6, F.155, V.156, E.157 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain B: K.48, R.182, I.183 Ligand excluded by PLIP SO4.14: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain B: D.72, D.73, R.136 Ligand excluded by PLIP SO4.16: 1 residues within 4Å: Chain B: R.327 Ligand excluded by PLIP SO4.17: 4 residues within 4Å: Chain B: K.53, E.215, R.256, N.260 Ligand excluded by PLIP SO4.18: 4 residues within 4Å: Chain B: M.1, K.2, E.3, L.4 Ligand excluded by PLIP SO4.21: 5 residues within 4Å: Chain C: K.2, R.6, F.155, V.156, E.157 Ligand excluded by PLIP SO4.22: 2 residues within 4Å: Chain C: K.271, Y.272 Ligand excluded by PLIP SO4.23: 5 residues within 4Å: Chain C: S.254, K.255, R.256 Chain D: E.19, G.40 Ligand excluded by PLIP SO4.24: 4 residues within 4Å: Chain C: V.71, D.72, D.73, R.136 Ligand excluded by PLIP SO4.25: 4 residues within 4Å: Chain C: M.1, K.2, E.3, L.4 Ligand excluded by PLIP SO4.28: 4 residues within 4Å: Chain D: K.2, R.6, V.156, E.157 Ligand excluded by PLIP SO4.29: 3 residues within 4Å: Chain D: D.72, D.73, R.136 Ligand excluded by PLIP SO4.30: 3 residues within 4Å: Chain D: I.270, K.271, Y.272 Ligand excluded by PLIP SO4.31: 4 residues within 4Å: Chain B: G.40 Chain D: S.254, K.255, R.256 Ligand excluded by PLIP SO4.32: 3 residues within 4Å: Chain D: G.200, L.201, M.285 Ligand excluded by PLIP SO4.33: 4 residues within 4Å: Chain D: M.1, K.2, E.3, L.4 Ligand excluded by PLIP SO4.37: 5 residues within 4Å: Chain E: K.2, R.6, F.155, V.156, E.157 Ligand excluded by PLIP SO4.38: 4 residues within 4Å: Chain E: G.40 Chain I: S.254, K.255, R.256 Ligand excluded by PLIP SO4.39: 4 residues within 4Å: Chain E: V.71, D.72, D.73, R.136 Ligand excluded by PLIP SO4.40: 1 residues within 4Å: Chain E: R.327 Ligand excluded by PLIP SO4.41: 2 residues within 4Å: Chain E: K.271, Y.272 Ligand excluded by PLIP SO4.42: 4 residues within 4Å: Chain E: M.1, K.2, E.3, L.4 Ligand excluded by PLIP SO4.45: 3 residues within 4Å: Chain F: S.254, K.255, R.256 Ligand excluded by PLIP SO4.46: 5 residues within 4Å: Chain F: K.2, R.6, F.155, V.156, E.157 Ligand excluded by PLIP SO4.47: 3 residues within 4Å: Chain F: K.48, R.182, I.183 Ligand excluded by PLIP SO4.48: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.49: 3 residues within 4Å: Chain F: D.72, D.73, R.136 Ligand excluded by PLIP SO4.50: 1 residues within 4Å: Chain F: R.327 Ligand excluded by PLIP SO4.51: 4 residues within 4Å: Chain F: K.53, E.215, R.256, N.260 Ligand excluded by PLIP SO4.52: 4 residues within 4Å: Chain F: M.1, K.2, E.3, L.4 Ligand excluded by PLIP SO4.55: 5 residues within 4Å: Chain G: K.2, R.6, F.155, V.156, E.157 Ligand excluded by PLIP SO4.56: 2 residues within 4Å: Chain G: K.271, Y.272 Ligand excluded by PLIP SO4.57: 5 residues within 4Å: Chain G: S.254, K.255, R.256 Chain H: E.19, G.40 Ligand excluded by PLIP SO4.58: 4 residues within 4Å: Chain G: V.71, D.72, D.73, R.136 Ligand excluded by PLIP SO4.59: 4 residues within 4Å: Chain G: M.1, K.2, E.3, L.4 Ligand excluded by PLIP SO4.62: 4 residues within 4Å: Chain H: K.2, R.6, V.156, E.157 Ligand excluded by PLIP SO4.63: 3 residues within 4Å: Chain H: D.72, D.73, R.136 Ligand excluded by PLIP SO4.64: 3 residues within 4Å: Chain H: I.270, K.271, Y.272 Ligand excluded by PLIP SO4.65: 4 residues within 4Å: Chain F: G.40 Chain H: S.254, K.255, R.256 Ligand excluded by PLIP SO4.66: 3 residues within 4Å: Chain H: G.200, L.201, M.285 Ligand excluded by PLIP SO4.67: 4 residues within 4Å: Chain H: M.1, K.2, E.3, L.4 Ligand excluded by PLIP SO4.71: 5 residues within 4Å: Chain I: K.2, R.6, F.155, V.156, E.157 Ligand excluded by PLIP SO4.72: 4 residues within 4Å: Chain A: S.254, K.255, R.256 Chain I: G.40 Ligand excluded by PLIP SO4.73: 4 residues within 4Å: Chain I: V.71, D.72, D.73, R.136 Ligand excluded by PLIP SO4.74: 1 residues within 4Å: Chain I: R.327 Ligand excluded by PLIP SO4.75: 2 residues within 4Å: Chain I: K.271, Y.272 Ligand excluded by PLIP SO4.76: 4 residues within 4Å: Chain I: M.1, K.2, E.3, L.4 Ligand excluded by PLIP SO4.79: 3 residues within 4Å: Chain J: S.254, K.255, R.256 Ligand excluded by PLIP SO4.80: 5 residues within 4Å: Chain J: K.2, R.6, F.155, V.156, E.157 Ligand excluded by PLIP SO4.81: 3 residues within 4Å: Chain J: K.48, R.182, I.183 Ligand excluded by PLIP SO4.82: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.83: 3 residues within 4Å: Chain J: D.72, D.73, R.136 Ligand excluded by PLIP SO4.84: 1 residues within 4Å: Chain J: R.327 Ligand excluded by PLIP SO4.85: 4 residues within 4Å: Chain J: K.53, E.215, R.256, N.260 Ligand excluded by PLIP SO4.86: 4 residues within 4Å: Chain J: M.1, K.2, E.3, L.4 Ligand excluded by PLIP SO4.89: 5 residues within 4Å: Chain K: K.2, R.6, F.155, V.156, E.157 Ligand excluded by PLIP SO4.90: 2 residues within 4Å: Chain K: K.271, Y.272 Ligand excluded by PLIP SO4.91: 5 residues within 4Å: Chain K: S.254, K.255, R.256 Chain L: E.19, G.40 Ligand excluded by PLIP SO4.92: 4 residues within 4Å: Chain K: V.71, D.72, D.73, R.136 Ligand excluded by PLIP SO4.93: 4 residues within 4Å: Chain K: M.1, K.2, E.3, L.4 Ligand excluded by PLIP SO4.96: 4 residues within 4Å: Chain L: K.2, R.6, V.156, E.157 Ligand excluded by PLIP SO4.97: 3 residues within 4Å: Chain L: D.72, D.73, R.136 Ligand excluded by PLIP SO4.98: 3 residues within 4Å: Chain L: I.270, K.271, Y.272 Ligand excluded by PLIP SO4.99: 4 residues within 4Å: Chain J: G.40 Chain L: S.254, K.255, R.256 Ligand excluded by PLIP SO4.100: 3 residues within 4Å: Chain L: G.200, L.201, M.285 Ligand excluded by PLIP SO4.101: 4 residues within 4Å: Chain L: M.1, K.2, E.3, L.4 Ligand excluded by PLIP

3 x OH: HYDROXIDE ION(Non-covalent)

OH.34: 7 residues within 4Å: Chain D: H.60, D.168, E.197, E.198, D.220 Ligands: ZN.26, CO.27 2 PLIP interactions: 2 interactions with chain D Water bridges: D:D.168, D:G.281 OH.68: 7 residues within 4Å: Chain H: H.60, D.168, E.197, E.198, D.220 Ligands: ZN.60, CO.61 2 PLIP interactions: 2 interactions with chain H Water bridges: H:D.168, H:G.281 OH.102: 7 residues within 4Å: Chain L: H.60, D.168, E.197, E.198, D.220 Ligands: ZN.94, CO.95 2 PLIP interactions: 2 interactions with chain L Water bridges: L:D.168, L:G.281

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dutoit, R. et al., How metal cofactors drive dimer-dodecamer transition of the M42 aminopeptidase TmPep1050 ofThermotoga maritima. J.Biol.Chem. (2019)

Release Date

2019-10-23

Peptides

Aminopeptidase: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
A

F
B

G
C

H
D

I
A

J
B

K
C

L
D

Aminopeptidase

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