SMTL ID : 6p2k.1

Crystal structure of AFV00434, an ancestral GH74 enzyme

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-hexamer

Ligands

18 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: E.559, D.562, D.566 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.559, A:D.562, A:D.566, A:D.566, H2O.5 ZN.2: 2 residues within 4Å: Chain A: Q.16, D.124 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.124, H2O.1, H2O.9, H2O.15 ZN.3: 3 residues within 4Å: Chain A: D.405, D.513, R.747 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.513, H2O.3, H2O.5, H2O.5, H2O.7 ZN.17: 3 residues within 4Å: Chain B: E.559, D.562, D.566 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.559, B:D.562, B:D.566, B:D.566, H2O.35 ZN.18: 2 residues within 4Å: Chain B: Q.16, D.124 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.124, H2O.32, H2O.40, H2O.45 ZN.19: 3 residues within 4Å: Chain B: D.405, D.513, R.747 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.513, H2O.34, H2O.36, H2O.36, H2O.38 ZN.33: 3 residues within 4Å: Chain C: E.559, D.562, D.566 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.559, C:D.562, C:D.566, C:D.566, H2O.66 ZN.34: 2 residues within 4Å: Chain C: Q.16, D.124 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.124, H2O.63, H2O.71, H2O.76 ZN.35: 3 residues within 4Å: Chain C: D.405, D.513, R.747 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:D.513, H2O.65, H2O.66, H2O.67, H2O.69 ZN.49: 3 residues within 4Å: Chain D: Q.16, Q.18, D.124 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:D.124, H2O.93, H2O.94, H2O.94, H2O.97 ZN.50: 2 residues within 4Å: Chain D: D.405, D.513 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:D.513, H2O.97, H2O.97, H2O.99, H2O.111 ZN.61: 2 residues within 4Å: Chain B: D.544 Chain D: D.544 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: B:D.544, D:D.544, H2O.52, H2O.54 ZN.62: 3 residues within 4Å: Chain E: Q.16, Q.18, D.124 5 PLIP interactions: 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: E:D.124, H2O.128, H2O.129, H2O.130, H2O.132 ZN.63: 2 residues within 4Å: Chain E: D.405, D.513 5 PLIP interactions: 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: E:D.513, H2O.132, H2O.132, H2O.134, H2O.146 ZN.74: 2 residues within 4Å: Chain C: D.544 Chain E: D.544 4 PLIP interactions: 1 interactions with chain E, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: E:D.544, C:D.544, H2O.83, H2O.85 ZN.75: 3 residues within 4Å: Chain F: Q.16, Q.18, D.124 5 PLIP interactions: 1 interactions with chain F, 4 Ligand-Water interactions Metal complexes: F:D.124, H2O.163, H2O.164, H2O.165, H2O.167 ZN.76: 2 residues within 4Å: Chain F: D.405, D.513 5 PLIP interactions: 1 interactions with chain F, 4 Ligand-Water interactions Metal complexes: F:D.513, H2O.167, H2O.167, H2O.169, H2O.181 ZN.87: 2 residues within 4Å: Chain A: D.544 Chain F: D.544 4 PLIP interactions: 1 interactions with chain F, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: F:D.544, A:D.544, H2O.21, H2O.23

42 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: Y.402, Y.404, A.418, G.471, G.472 Ligand excluded by PLIP GOL.5: 3 residues within 4Å: Chain A: R.289, Q.355, Y.470 Ligand excluded by PLIP GOL.6: 3 residues within 4Å: Chain A: N.71, N.86, G.87 Ligand excluded by PLIP GOL.10: 1 residues within 4Å: Chain A: W.616 Ligand excluded by PLIP GOL.11: 2 residues within 4Å: Chain A: V.341, T.342 Ligand excluded by PLIP GOL.12: 3 residues within 4Å: Chain A: W.681, N.682, N.686 Ligand excluded by PLIP GOL.13: 5 residues within 4Å: Chain A: R.438, G.440, G.441, G.442, N.444 Ligand excluded by PLIP GOL.14: 2 residues within 4Å: Chain A: N.647, P.666 Ligand excluded by PLIP GOL.15: 6 residues within 4Å: Chain A: Q.7, L.9, G.428, V.430, D.751, R.768 Ligand excluded by PLIP GOL.20: 5 residues within 4Å: Chain B: Y.402, Y.404, A.418, G.471, G.472 Ligand excluded by PLIP GOL.21: 3 residues within 4Å: Chain B: R.289, Q.355, Y.470 Ligand excluded by PLIP GOL.22: 3 residues within 4Å: Chain B: N.71, N.86, G.87 Ligand excluded by PLIP GOL.26: 1 residues within 4Å: Chain B: W.616 Ligand excluded by PLIP GOL.27: 2 residues within 4Å: Chain B: V.341, T.342 Ligand excluded by PLIP GOL.28: 3 residues within 4Å: Chain B: W.681, N.682, N.686 Ligand excluded by PLIP GOL.29: 5 residues within 4Å: Chain B: R.438, G.440, G.441, G.442, N.444 Ligand excluded by PLIP GOL.30: 2 residues within 4Å: Chain B: N.647, P.666 Ligand excluded by PLIP GOL.31: 6 residues within 4Å: Chain B: Q.7, L.9, G.428, V.430, D.751, R.768 Ligand excluded by PLIP GOL.36: 5 residues within 4Å: Chain C: Y.402, Y.404, A.418, G.471, G.472 Ligand excluded by PLIP GOL.37: 3 residues within 4Å: Chain C: R.289, Q.355, Y.470 Ligand excluded by PLIP GOL.38: 3 residues within 4Å: Chain C: N.71, N.86, G.87 Ligand excluded by PLIP GOL.42: 1 residues within 4Å: Chain C: W.616 Ligand excluded by PLIP GOL.43: 2 residues within 4Å: Chain C: V.341, T.342 Ligand excluded by PLIP GOL.44: 3 residues within 4Å: Chain C: W.681, N.682, N.686 Ligand excluded by PLIP GOL.45: 5 residues within 4Å: Chain C: R.438, G.440, G.441, G.442, N.444 Ligand excluded by PLIP GOL.46: 2 residues within 4Å: Chain C: N.647, P.666 Ligand excluded by PLIP GOL.47: 6 residues within 4Å: Chain C: Q.7, L.9, G.428, V.430, D.751, R.768 Ligand excluded by PLIP GOL.52: 1 residues within 4Å: Chain D: W.616 Ligand excluded by PLIP GOL.53: 5 residues within 4Å: Chain D: Y.402, Y.404, A.418, G.471, G.472 Ligand excluded by PLIP GOL.54: 3 residues within 4Å: Chain D: G.129, K.130, Y.712 Ligand excluded by PLIP GOL.55: 3 residues within 4Å: Chain D: N.113, Q.145, N.146 Ligand excluded by PLIP GOL.56: 3 residues within 4Å: Chain D: W.681, G.685, N.686 Ligand excluded by PLIP GOL.65: 1 residues within 4Å: Chain E: W.616 Ligand excluded by PLIP GOL.66: 5 residues within 4Å: Chain E: Y.402, Y.404, A.418, G.471, G.472 Ligand excluded by PLIP GOL.67: 3 residues within 4Å: Chain E: G.129, K.130, Y.712 Ligand excluded by PLIP GOL.68: 3 residues within 4Å: Chain E: N.113, Q.145, N.146 Ligand excluded by PLIP GOL.69: 3 residues within 4Å: Chain E: W.681, G.685, N.686 Ligand excluded by PLIP GOL.78: 1 residues within 4Å: Chain F: W.616 Ligand excluded by PLIP GOL.79: 5 residues within 4Å: Chain F: Y.402, Y.404, A.418, G.471, G.472 Ligand excluded by PLIP GOL.80: 3 residues within 4Å: Chain F: G.129, K.130, Y.712 Ligand excluded by PLIP GOL.81: 3 residues within 4Å: Chain F: N.113, Q.145, N.146 Ligand excluded by PLIP GOL.82: 3 residues within 4Å: Chain F: W.681, G.685, N.686 Ligand excluded by PLIP

18 x PE3: 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL(Non-functional Binders)

PE3.7: 6 residues within 4Å: Chain A: I.453, A.454, D.455, G.458, P.460, P.521 Ligand excluded by PLIP PE3.8: 5 residues within 4Å: Chain A: I.51, T.52, N.54, N.89, H.739 Ligand excluded by PLIP PE3.9: 7 residues within 4Å: Chain A: W.457, G.458 Chain E: N.411, D.427, T.486, H.487, S.488 Ligand excluded by PLIP PE3.23: 6 residues within 4Å: Chain B: I.453, A.454, D.455, G.458, P.460, P.521 Ligand excluded by PLIP PE3.24: 5 residues within 4Å: Chain B: I.51, T.52, N.54, N.89, H.739 Ligand excluded by PLIP PE3.25: 7 residues within 4Å: Chain B: W.457, G.458 Chain F: N.411, D.427, T.486, H.487, S.488 Ligand excluded by PLIP PE3.39: 6 residues within 4Å: Chain C: I.453, A.454, D.455, G.458, P.460, P.521 Ligand excluded by PLIP PE3.40: 5 residues within 4Å: Chain C: I.51, T.52, N.54, N.89, H.739 Ligand excluded by PLIP PE3.41: 7 residues within 4Å: Chain C: W.457, G.458 Chain D: N.411, D.427, T.486, H.487, S.488 Ligand excluded by PLIP PE3.57: 4 residues within 4Å: Chain D: I.453, A.454, D.455, P.460 Ligand excluded by PLIP PE3.58: 4 residues within 4Å: Chain D: T.52, N.54, N.89, H.739 Ligand excluded by PLIP PE3.59: 7 residues within 4Å: Chain D: R.263, K.287, D.288, R.289, N.354, Q.355, Y.470 Ligand excluded by PLIP PE3.70: 4 residues within 4Å: Chain E: I.453, A.454, D.455, P.460 Ligand excluded by PLIP PE3.71: 4 residues within 4Å: Chain E: T.52, N.54, N.89, H.739 Ligand excluded by PLIP PE3.72: 7 residues within 4Å: Chain E: R.263, K.287, D.288, R.289, N.354, Q.355, Y.470 Ligand excluded by PLIP PE3.83: 4 residues within 4Å: Chain F: I.453, A.454, D.455, P.460 Ligand excluded by PLIP PE3.84: 4 residues within 4Å: Chain F: T.52, N.54, N.89, H.739 Ligand excluded by PLIP PE3.85: 7 residues within 4Å: Chain F: R.263, K.287, D.288, R.289, N.354, Q.355, Y.470 Ligand excluded by PLIP

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

CL.16: 3 residues within 4Å: Chain A: K.693, Y.708, H.710 Ligand excluded by PLIP CL.32: 3 residues within 4Å: Chain B: K.693, Y.708, H.710 Ligand excluded by PLIP CL.48: 3 residues within 4Å: Chain C: K.693, Y.708, H.710 Ligand excluded by PLIP CL.60: 5 residues within 4Å: Chain D: E.229 Chain F: Q.254, V.255, T.256, G.257 Ligand excluded by PLIP CL.73: 5 residues within 4Å: Chain D: Q.254, V.255, T.256, G.257 Chain E: E.229 Ligand excluded by PLIP CL.86: 5 residues within 4Å: Chain E: Q.254, V.255, T.256, G.257 Chain F: E.229 Ligand excluded by PLIP

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.51: 8 residues within 4Å: Chain D: D.125, Y.167, N.184, W.210, K.212, K.231, P.232, L.234 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:W.210 Hydrogen bonds: D:N.184, D:K.231 Water bridges: D:N.165, D:N.165, D:K.231 Salt bridges: D:K.212 ACT.64: 8 residues within 4Å: Chain E: D.125, Y.167, N.184, W.210, K.212, K.231, P.232, L.234 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:W.210 Hydrogen bonds: E:N.184, E:K.231 Water bridges: E:N.165, E:N.165, E:K.231 Salt bridges: E:K.212 ACT.77: 8 residues within 4Å: Chain F: D.125, Y.167, N.184, W.210, K.212, K.231, P.232, L.234 7 PLIP interactions: 7 interactions with chain F Hydrophobic interactions: F:W.210 Hydrogen bonds: F:N.184, F:K.231 Water bridges: F:N.165, F:N.165, F:K.231 Salt bridges: F:K.212

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arnal, G. et al., Substrate specificity, regiospecificity, and processivity in glycoside hydrolase family 74. J.Biol.Chem. (2019)

Release Date

2019-07-31

Peptides

Fibronectin type III domain-containing protein: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

C
B

D
A

E
A

F
A

Fibronectin type III domain-containing protein