SMTL ID : 2p7h.3 (2 other biounits)

Crystal structure of a sam dependent methyl-transferase type 12 family protein (eca1738) from pectobacterium atrosepticum scri1043 at 1.85 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-octamer

Ligands

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

CL.1: 1 residues within 4Å: Chain A: V.164 Ligand excluded by PLIP CL.2: 2 residues within 4Å: Chain A: A.132, E.133 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain B: A.132, E.133 Ligand excluded by PLIP CL.13: 1 residues within 4Å: Chain C: V.164 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain C: A.132, E.133 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain D: A.132, E.133 Ligand excluded by PLIP CL.25: 2 residues within 4Å: Chain E: C.175, R.184 Ligand excluded by PLIP CL.28: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.31: 2 residues within 4Å: Chain G: C.175, R.184 Ligand excluded by PLIP CL.34: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

4 x NA: SODIUM ION(Non-functional Binders)

NA.3: 5 residues within 4Å: Chain A: H.115, I.116, D.117 Chain E: N.249, Q.250 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain A Hydrogen bonds: E:Q.250, A:D.117, A:D.117 Water bridges: E:N.249 NA.8: 4 residues within 4Å: Chain B: H.115, D.117 Chain H: N.249, Q.250 5 PLIP interactions: 2 interactions with chain H, 3 interactions with chain B Hydrogen bonds: H:Q.250, H:Q.250, B:H.115, B:D.117 Water bridges: B:R.174 NA.15: 5 residues within 4Å: Chain C: H.115, I.116, D.117 Chain G: N.249, Q.250 4 PLIP interactions: 3 interactions with chain G, 1 interactions with chain C Hydrogen bonds: G:Q.250, G:Q.250, C:D.117 Water bridges: G:N.249 NA.20: 4 residues within 4Å: Chain D: H.115, D.117 Chain F: N.249, Q.250 5 PLIP interactions: 2 interactions with chain F, 3 interactions with chain D Hydrogen bonds: F:Q.250, F:Q.250, D:D.117, D:D.117 Water bridges: D:R.174

8 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.4: 8 residues within 4Å: Chain A: H.30, E.48, G.50, S.51, F.52, F.56, T.110, V.112 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:H.30, A:E.48, A:S.51, A:F.56, A:T.110, A:T.110 Water bridges: A:G.54, A:D.55, A:T.110 TRS.9: 7 residues within 4Å: Chain B: H.30, E.48, G.50, F.52, F.56, T.110, V.112 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:E.48, B:E.48, B:G.50, B:S.51, B:F.56 Water bridges: B:H.30, B:G.54, B:D.55, B:T.110 TRS.16: 8 residues within 4Å: Chain C: H.30, E.48, G.50, S.51, F.52, F.56, T.110, V.112 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:H.30, C:E.48, C:S.51, C:F.56, C:T.110, C:T.110 Water bridges: C:G.54, C:D.55, C:T.110 TRS.21: 7 residues within 4Å: Chain D: H.30, E.48, G.50, F.52, F.56, T.110, V.112 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:E.48, D:E.48, D:G.50, D:S.51, D:F.56 Water bridges: D:H.30, D:G.54, D:D.55, D:T.110 TRS.26: 7 residues within 4Å: Chain E: E.48, G.50, S.51, F.52, F.56, T.110, V.112 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:E.48, E:S.51, E:F.56, E:T.110, E:T.110 Water bridges: E:H.30, E:G.54, E:G.54, E:T.110 TRS.29: 7 residues within 4Å: Chain F: E.48, G.50, S.51, F.52, F.56, T.110, V.112 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:E.48, F:E.48, F:S.51, F:F.56, F:T.110 Water bridges: F:H.30, F:G.54, F:D.55, F:T.110 TRS.32: 7 residues within 4Å: Chain G: E.48, G.50, S.51, F.52, F.56, T.110, V.112 9 PLIP interactions: 9 interactions with chain G Hydrogen bonds: G:E.48, G:S.51, G:F.56, G:T.110, G:T.110 Water bridges: G:H.30, G:G.54, G:G.54, G:T.110 TRS.35: 7 residues within 4Å: Chain H: E.48, G.50, S.51, F.52, F.56, T.110, V.112 9 PLIP interactions: 9 interactions with chain H Hydrogen bonds: H:E.48, H:E.48, H:S.51, H:F.56, H:T.110 Water bridges: H:H.30, H:G.54, H:D.55, H:T.110

14 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 4 residues within 4Å: Chain A: R.42, P.43, H.63, F.64 No protein-ligand interaction detected (PLIP) EDO.6: 5 residues within 4Å: Chain A: P.142, R.149, E.168, H.173, T.176 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.149, A:H.173 Water bridges: A:N.143, A:A.238, A:A.238 EDO.10: 5 residues within 4Å: Chain B: L.100, R.102, R.103, D.129, W.130 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.100 Water bridges: B:R.103, B:R.125, B:D.129 EDO.11: 3 residues within 4Å: Chain B: H.160, S.162, A.163 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.162 EDO.12: 5 residues within 4Å: Chain B: P.142, N.143, R.149, H.173, T.176 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.149, B:H.173 Water bridges: B:N.143, B:E.168, B:T.176, B:T.176, B:A.238 EDO.17: 4 residues within 4Å: Chain C: R.42, P.43, H.63, F.64 No protein-ligand interaction detected (PLIP) EDO.18: 5 residues within 4Å: Chain C: P.142, R.149, E.168, H.173, T.176 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.149, C:H.173 Water bridges: C:N.143, C:A.238, C:A.238 EDO.22: 5 residues within 4Å: Chain D: L.100, R.102, R.103, D.129, W.130 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:L.100 Water bridges: D:R.103, D:R.125, D:D.129 EDO.23: 3 residues within 4Å: Chain D: H.160, S.162, A.163 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.162 EDO.24: 5 residues within 4Å: Chain D: P.142, N.143, R.149, H.173, T.176 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:R.149, D:H.173 Water bridges: D:N.143, D:E.168, D:T.176, D:T.176, D:A.238 EDO.27: 6 residues within 4Å: Chain E: P.142, N.143, R.149, E.168, H.173, T.176 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:R.149, E:H.173 Water bridges: E:N.143, E:A.238 EDO.30: 5 residues within 4Å: Chain F: P.142, R.149, E.168, H.173, T.176 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:R.149, F:H.173 Water bridges: F:N.143, F:E.168, F:T.176, F:A.238 EDO.33: 6 residues within 4Å: Chain G: P.142, N.143, R.149, E.168, H.173, T.176 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:R.149, G:H.173 Water bridges: G:N.143, G:A.238 EDO.36: 5 residues within 4Å: Chain H: P.142, R.149, E.168, H.173, T.176 6 PLIP interactions: 6 interactions with chain H Hydrogen bonds: H:R.149, H:H.173 Water bridges: H:N.143, H:E.168, H:T.176, H:A.238

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of hypothetical protein (YP_049838.1) from Erwinia carotovora atroseptica SCRI1043 at 1.85 A resolution. To be published

Release Date

2007-04-03

Peptides

Hypothetical protein: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

C
B

D
D

E
A

F
C

G
A

H
C

Hypothetical protein

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