SMTL ID : 5ds0.1

Crystal structure of TET aminopeptidase from marine sediment archaeon Thaumarchaeota archaeon SCGC AB-539-E09

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-12-mer

Ligands

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

CO.1: 5 residues within 4Å: Chain A: D.180, E.214, E.215, H.325 Ligands: CO.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.180, A:E.215, A:E.215, A:H.325 CO.2: 6 residues within 4Å: Chain A: H.66, D.180, E.214, E.215, E.237 Ligands: CO.1 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.66, A:D.180, A:E.214, A:E.237, A:E.237 CO.4: 5 residues within 4Å: Chain B: D.180, E.214, E.215, H.325 Ligands: CO.5 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.180, B:E.215, B:E.215, B:H.325 CO.5: 6 residues within 4Å: Chain B: H.66, D.180, E.214, E.215, E.237 Ligands: CO.4 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:H.66, B:D.180, B:E.214, B:E.237, B:E.237 CO.8: 6 residues within 4Å: Chain C: H.66, D.180, E.214, E.215, E.237 Ligands: CO.9 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:H.66, C:D.180, C:E.214, C:E.237, C:E.237 CO.9: 5 residues within 4Å: Chain C: D.180, E.214, E.215, H.325 Ligands: CO.8 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.180, C:E.215, C:E.215, C:H.325 CO.12: 6 residues within 4Å: Chain D: H.66, D.180, E.214, E.215, E.237 Ligands: CO.13 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:H.66, D:D.180, D:E.214, D:E.237, D:E.237 CO.13: 5 residues within 4Å: Chain D: D.180, E.214, E.215, H.325 Ligands: CO.12 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.180, D:E.215, D:E.215, D:H.325 CO.14: 7 residues within 4Å: Chain E: H.66, D.180, D.181, E.214, E.215, E.237 Ligands: CO.15 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:H.66, E:D.180, E:E.214, E:E.237, E:E.237 CO.15: 5 residues within 4Å: Chain E: D.180, E.214, E.215, H.325 Ligands: CO.14 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.180, E:E.215, E:E.215, E:H.325 CO.17: 5 residues within 4Å: Chain F: D.180, E.214, E.215, H.325 Ligands: CO.18 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.180, F:E.215, F:E.215, F:H.325 CO.18: 6 residues within 4Å: Chain F: H.66, D.180, E.214, E.215, E.237 Ligands: CO.17 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:H.66, F:D.180, F:E.214, F:E.237, F:E.237 CO.19: 6 residues within 4Å: Chain G: H.66, D.180, E.214, E.215, E.237 Ligands: CO.20 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:H.66, G:D.180, G:E.214, G:E.237, G:E.237 CO.20: 5 residues within 4Å: Chain G: D.180, E.214, E.215, H.325 Ligands: CO.19 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:D.180, G:E.215, G:E.215, G:H.325 CO.23: 5 residues within 4Å: Chain H: D.180, E.214, E.215, H.325 Ligands: CO.24 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:D.180, H:E.215, H:E.215, H:H.325 CO.24: 6 residues within 4Å: Chain H: H.66, D.180, E.214, E.215, E.237 Ligands: CO.23 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:H.66, H:D.180, H:E.237, H:E.237 CO.27: 5 residues within 4Å: Chain I: D.180, E.214, E.215, H.325 Ligands: CO.28 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:D.180, I:E.215, I:E.215, I:H.325 CO.28: 6 residues within 4Å: Chain I: H.66, D.180, E.214, E.215, E.237 Ligands: CO.27 5 PLIP interactions: 5 interactions with chain I Metal complexes: I:H.66, I:D.180, I:E.214, I:E.237, I:E.237 CO.31: 5 residues within 4Å: Chain J: D.180, E.214, E.215, H.325 Ligands: CO.32 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:D.180, J:E.215, J:E.215, J:H.325 CO.32: 6 residues within 4Å: Chain J: H.66, D.180, E.214, E.215, E.237 Ligands: CO.31 5 PLIP interactions: 5 interactions with chain J Metal complexes: J:H.66, J:D.180, J:E.214, J:E.237, J:E.237 CO.34: 5 residues within 4Å: Chain K: D.180, E.214, E.215, H.325 Ligands: CO.35 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:D.180, K:E.215, K:E.215, K:H.325 CO.35: 6 residues within 4Å: Chain K: H.66, D.180, E.214, E.215, E.237 Ligands: CO.34 5 PLIP interactions: 5 interactions with chain K Metal complexes: K:H.66, K:D.180, K:E.214, K:E.237, K:E.237 CO.37: 5 residues within 4Å: Chain L: D.180, E.214, E.215, H.325 Ligands: CO.38 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:D.180, L:E.215, L:E.215, L:H.325 CO.38: 7 residues within 4Å: Chain L: H.66, D.180, D.181, E.214, E.215, E.237 Ligands: CO.37 5 PLIP interactions: 5 interactions with chain L Metal complexes: L:H.66, L:D.180, L:E.214, L:E.237, L:E.237

15 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: E.15, P.161, W.162, S.163, P.164, K.177 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.15, A:P.161, A:S.163 GOL.6: 5 residues within 4Å: Chain B: E.15, W.162, S.163, P.164, K.177 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.163, B:S.163 GOL.7: 7 residues within 4Å: Chain B: A.115, S.116, P.118 Chain D: W.92, H.323, I.324, S.326 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:S.116, D:S.326, D:S.326 GOL.10: 5 residues within 4Å: Chain C: E.15, W.162, S.163, P.164, K.177 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.163 GOL.11: 8 residues within 4Å: Chain C: I.114, A.115, S.116, K.117, P.118 Chain L: W.92, H.323, I.324 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain L Hydrogen bonds: C:I.114, C:S.116, C:S.116, L:H.323, L:I.324 GOL.16: 7 residues within 4Å: Chain E: H.323, I.324, S.326 Chain F: I.114, A.115, S.116, P.118 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:I.114, E:I.324, E:S.326 GOL.21: 5 residues within 4Å: Chain A: H.323 Chain G: I.114, A.115, S.116, P.118 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:I.114, G:S.116 GOL.22: 6 residues within 4Å: Chain G: E.15, P.161, W.162, S.163, P.164, K.177 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:P.161, G:S.163 GOL.25: 4 residues within 4Å: Chain H: E.15, W.162, S.163, K.177 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:E.15, H:P.161, H:S.163 GOL.26: 7 residues within 4Å: Chain H: G.98, I.113, I.114, A.115, S.116, P.118 Chain I: H.323 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:G.98, H:S.116 GOL.29: 5 residues within 4Å: Chain I: E.15, P.161, W.162, S.163, K.177 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:P.161 GOL.30: 6 residues within 4Å: Chain H: H.323, I.324, S.326 Chain I: A.115, S.116, P.118 4 PLIP interactions: 3 interactions with chain H, 1 interactions with chain I Hydrogen bonds: H:H.323, H:I.324, H:S.326, I:S.116 GOL.33: 6 residues within 4Å: Chain J: E.15, P.161, W.162, S.163, P.164, K.177 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:P.161, J:S.163 GOL.36: 7 residues within 4Å: Chain J: I.114, A.115, S.116, P.118 Chain K: H.323, I.324, S.326 5 PLIP interactions: 2 interactions with chain J, 3 interactions with chain K Hydrogen bonds: J:I.114, J:S.116, K:H.323, K:I.324, K:S.326 GOL.39: 6 residues within 4Å: Chain C: H.323 Chain L: I.114, A.115, S.116, K.117, P.118 3 PLIP interactions: 2 interactions with chain L, 1 interactions with chain C Hydrogen bonds: L:I.114, L:S.116, C:H.323

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Michalska, K. et al., Crystal structure of TET aminopeptidase from marine sediment archaeon Thaumarchaeota archaeon SCGC AB-539-E09. To Be Published

Release Date

2015-10-14

Peptides

Peptidase M42: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

Peptidase M42