SMTL ID : 2p7h.2 (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-16-mer

Ligands

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

CL.1: 2 residues within 4Å: Chain A: C.175, R.184 Ligand excluded by PLIP CL.4: 1 residues within 4Å: Chain B: V.164 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain B: A.132, E.133 Ligand excluded by PLIP CL.10: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain D: A.132, E.133 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain E: C.175, R.184 Ligand excluded by PLIP CL.22: 1 residues within 4Å: Chain F: V.164 Ligand excluded by PLIP CL.23: 2 residues within 4Å: Chain F: A.132, E.133 Ligand excluded by PLIP CL.28: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.31: 2 residues within 4Å: Chain H: A.132, E.133 Ligand excluded by PLIP CL.37: 2 residues within 4Å: Chain I: C.175, R.184 Ligand excluded by PLIP CL.40: 1 residues within 4Å: Chain J: V.164 Ligand excluded by PLIP CL.41: 2 residues within 4Å: Chain J: A.132, E.133 Ligand excluded by PLIP CL.46: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.49: 2 residues within 4Å: Chain L: A.132, E.133 Ligand excluded by PLIP CL.55: 2 residues within 4Å: Chain M: C.175, R.184 Ligand excluded by PLIP CL.58: 1 residues within 4Å: Chain N: V.164 Ligand excluded by PLIP CL.59: 2 residues within 4Å: Chain N: A.132, E.133 Ligand excluded by PLIP CL.64: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.67: 2 residues within 4Å: Chain P: A.132, E.133 Ligand excluded by PLIP

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

TRS.2: 7 residues within 4Å: Chain A: E.48, G.50, S.51, F.52, F.56, T.110, V.112 Ligand excluded by PLIP TRS.7: 8 residues within 4Å: Chain B: H.30, E.48, G.50, S.51, F.52, F.56, T.110, V.112 Ligand excluded by PLIP TRS.11: 7 residues within 4Å: Chain C: E.48, G.50, S.51, F.52, F.56, T.110, V.112 Ligand excluded by PLIP TRS.15: 7 residues within 4Å: Chain D: H.30, E.48, G.50, F.52, F.56, T.110, V.112 Ligand excluded by PLIP TRS.20: 7 residues within 4Å: Chain E: E.48, G.50, S.51, F.52, F.56, T.110, V.112 Ligand excluded by PLIP TRS.25: 8 residues within 4Å: Chain F: H.30, E.48, G.50, S.51, F.52, F.56, T.110, V.112 Ligand excluded by PLIP TRS.29: 7 residues within 4Å: Chain G: E.48, G.50, S.51, F.52, F.56, T.110, V.112 Ligand excluded by PLIP TRS.33: 7 residues within 4Å: Chain H: H.30, E.48, G.50, F.52, F.56, T.110, V.112 Ligand excluded by PLIP TRS.38: 7 residues within 4Å: Chain I: E.48, G.50, S.51, F.52, F.56, T.110, V.112 Ligand excluded by PLIP TRS.43: 8 residues within 4Å: Chain J: H.30, E.48, G.50, S.51, F.52, F.56, T.110, V.112 Ligand excluded by PLIP TRS.47: 7 residues within 4Å: Chain K: E.48, G.50, S.51, F.52, F.56, T.110, V.112 Ligand excluded by PLIP TRS.51: 7 residues within 4Å: Chain L: H.30, E.48, G.50, F.52, F.56, T.110, V.112 Ligand excluded by PLIP TRS.56: 7 residues within 4Å: Chain M: E.48, G.50, S.51, F.52, F.56, T.110, V.112 Ligand excluded by PLIP TRS.61: 8 residues within 4Å: Chain N: H.30, E.48, G.50, S.51, F.52, F.56, T.110, V.112 Ligand excluded by PLIP TRS.65: 7 residues within 4Å: Chain O: E.48, G.50, S.51, F.52, F.56, T.110, V.112 Ligand excluded by PLIP TRS.69: 7 residues within 4Å: Chain P: H.30, E.48, G.50, F.52, F.56, T.110, V.112 Ligand excluded by PLIP

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

EDO.3: 6 residues within 4Å: Chain A: P.142, N.143, R.149, E.168, H.173, T.176 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain B: R.42, P.43, H.63, F.64 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain B: P.142, R.149, E.168, H.173, T.176 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain C: P.142, R.149, E.168, H.173, T.176 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain D: L.100, R.102, R.103, D.129, W.130 Ligand excluded by PLIP EDO.17: 3 residues within 4Å: Chain D: H.160, S.162, A.163 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain D: P.142, N.143, R.149, H.173, T.176 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain E: P.142, N.143, R.149, E.168, H.173, T.176 Ligand excluded by PLIP EDO.26: 4 residues within 4Å: Chain F: R.42, P.43, H.63, F.64 Ligand excluded by PLIP EDO.27: 5 residues within 4Å: Chain F: P.142, R.149, E.168, H.173, T.176 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain G: P.142, R.149, E.168, H.173, T.176 Ligand excluded by PLIP EDO.34: 5 residues within 4Å: Chain H: L.100, R.102, R.103, D.129, W.130 Ligand excluded by PLIP EDO.35: 3 residues within 4Å: Chain H: H.160, S.162, A.163 Ligand excluded by PLIP EDO.36: 5 residues within 4Å: Chain H: P.142, N.143, R.149, H.173, T.176 Ligand excluded by PLIP EDO.39: 6 residues within 4Å: Chain I: P.142, N.143, R.149, E.168, H.173, T.176 Ligand excluded by PLIP EDO.44: 4 residues within 4Å: Chain J: R.42, P.43, H.63, F.64 Ligand excluded by PLIP EDO.45: 5 residues within 4Å: Chain J: P.142, R.149, E.168, H.173, T.176 Ligand excluded by PLIP EDO.48: 5 residues within 4Å: Chain K: P.142, R.149, E.168, H.173, T.176 Ligand excluded by PLIP EDO.52: 5 residues within 4Å: Chain L: L.100, R.102, R.103, D.129, W.130 Ligand excluded by PLIP EDO.53: 3 residues within 4Å: Chain L: H.160, S.162, A.163 Ligand excluded by PLIP EDO.54: 5 residues within 4Å: Chain L: P.142, N.143, R.149, H.173, T.176 Ligand excluded by PLIP EDO.57: 6 residues within 4Å: Chain M: P.142, N.143, R.149, E.168, H.173, T.176 Ligand excluded by PLIP EDO.62: 4 residues within 4Å: Chain N: R.42, P.43, H.63, F.64 Ligand excluded by PLIP EDO.63: 5 residues within 4Å: Chain N: P.142, R.149, E.168, H.173, T.176 Ligand excluded by PLIP EDO.66: 5 residues within 4Å: Chain O: P.142, R.149, E.168, H.173, T.176 Ligand excluded by PLIP EDO.70: 5 residues within 4Å: Chain P: L.100, R.102, R.103, D.129, W.130 Ligand excluded by PLIP EDO.71: 3 residues within 4Å: Chain P: H.160, S.162, A.163 Ligand excluded by PLIP EDO.72: 5 residues within 4Å: Chain P: P.142, N.143, R.149, H.173, T.176 Ligand excluded by PLIP

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

NA.6: 5 residues within 4Å: Chain B: H.115, I.116, D.117 Chain I: N.249, Q.250 4 PLIP interactions: 2 interactions with chain I, 2 interactions with chain B Hydrogen bonds: I:Q.250, B:D.117, B:D.117 Water bridges: I:N.249 NA.14: 4 residues within 4Å: Chain D: H.115, D.117 Chain O: N.249, Q.250 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain O Hydrogen bonds: D:H.115, D:D.117, O:Q.250, O:Q.250 Water bridges: D:R.174 NA.24: 5 residues within 4Å: Chain F: H.115, I.116, D.117 Chain M: N.249, Q.250 4 PLIP interactions: 3 interactions with chain M, 1 interactions with chain F Hydrogen bonds: M:N.249, M:Q.250, F:D.117 Water bridges: M:N.249 NA.32: 4 residues within 4Å: Chain H: H.115, D.117 Chain K: N.249, Q.250 5 PLIP interactions: 3 interactions with chain K, 2 interactions with chain H Hydrogen bonds: K:N.249, K:Q.250, K:Q.250, H:D.117 Water bridges: H:R.174 NA.42: 5 residues within 4Å: Chain E: N.249, Q.250 Chain J: H.115, I.116, D.117 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain J Hydrogen bonds: E:Q.250, J:D.117, J:D.117 Water bridges: E:N.249 NA.50: 4 residues within 4Å: Chain C: N.249, Q.250 Chain L: H.115, D.117 5 PLIP interactions: 3 interactions with chain L, 2 interactions with chain C Hydrogen bonds: L:D.117, L:D.117, C:Q.250, C:Q.250 Water bridges: L:R.174 NA.60: 5 residues within 4Å: Chain A: N.249, Q.250 Chain N: H.115, I.116, D.117 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain N Hydrogen bonds: A:N.249, A:Q.250, N:D.117 Water bridges: A:N.249 NA.68: 4 residues within 4Å: Chain G: N.249, Q.250 Chain P: H.115, D.117 5 PLIP interactions: 2 interactions with chain G, 3 interactions with chain P Hydrogen bonds: G:Q.250, G:Q.250, P:H.115, P:D.117 Water bridges: P:R.174

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: ABCDEFGHIJKLMNOP

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

M
A

N
B

O
C

P
D

Hypothetical protein

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